Statistics Summary Report for S2F Center

Last updated: Feb 2 2012

• Target Status Statistics
• Table 1: Status Statistics for S2F
• Table 2: Status Statistics for S2F by Organisms
• Deposited Structure Statistics
• Table 3: PDB Status Statistics for Structures from S2F
• Table 4: List of Structures Deposited by S2F in the PDB
• Sequence Redundancy Statistics
• Table 5: Sequence Redundancy Statistics for S2F by Experimental Status
• Table 6: Sequence Redundancy Statistics for Structures Released by S2F in the PDB by Year

Target Status Statistics

Total number of targets deposited by S2F to TargetDB: 336

      View S2F Target List

Table 1: Status Statistics for S2F

Status	Total Number of Targets	(%) Relative to "Cloned" Targets	(%) Relative to "Expressed" Targets	(%) Relative to "Purified" Targets	(%) Relative to "Crystallized" Targets
Cloned	310	100.0	-	-	-
Expressed	174	56.1	100.0	-	-
Soluble	0	0.0	0.0	-	-
Purified	117	37.7	67.2	100.0	-
Crystallized	45	14.5	25.9	38.5	100.0
Diffraction-quality Crystals	0	0.0	0.0	0.0	0.0
Diffraction	40	12.9	23.0	34.2	88.9
NMR Assigned	0	0.0	0.0	0.0	-
HSQC	9	2.9	5.2	7.7	-
Crystal Structure	1	0.3	0.6	0.9	2.2
NMR Structure	1	0.3	0.6	0.9	-
In PDB1	44	14.2	25.3	37.6	96
Work Stopped	0	-	-	-	-
Test Target	0	-	-	-	-
Other	0	-	-	-	-

Last updated: Feb 2 2012

Note 1:   Number of targets with status "in PDB" may not be equal to number of structures determined by a project. A target may reference several PDB IDs (example: structure of the same polypeptides with different ligands). Multiple targets in TargetDB may identify the same PDB structure when a stucture is a result of collaboration between different centers and each center includes the target on its target list.

Table 2: Status Statistics for S2F by Organism

These statistics are derived from mapping of target sequences to GenBank using >=98% sequence identity cut off.

Organism	Total Number1	Work Stopped	Cloned	Expressed	Purified	Crystallized	Crystal Structure	NMR Structure	In PDB
Bacteria	336	0	310	174	117	45	1	1	44
Prokaryota	336	0	310	174	117	45	1	1	44
Uncultured or unidentified	4	0	4	2	2	0	0	0	0

Last updated: Feb 2 2012

Note 1:   Total counts in this table may differ from total number of targets and structures. A target is counted in different organism specifications if:
- a target is mapped to different organisms
- a target is a hybrid complex (for example:a complex of human and mouse polypeptides).

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Deposited Structure Statistics for S2F Center

Number of Released X-Ray Structures: 44

Number of Released NMR Structures: 7

Total number of released structures from S2F center in the PDB: 51

Table 3: PDB Status Statistics for Structures from S2F

PDB Status	Number of Structures
Total Deposited	51
Released	51
Release on Publication	0
Release on Certain Date	0
In Process	0

Last updated: Feb 2 2012

Note 1:   "Total Deposited" are all structures in the PDB including structures released to the public and structures that are in the process to be released ("Released on Publication" , "Released on Certain Date", etc.).

Table 4: List of Structures Deposited in the PDB by S2F

Total number of structures: 51

Structures of distinct targets: 441

1   A target may reference several PDB IDs (example: structure of the same polypeptides with different ligands).
In this case only one structure is counted to compute number of structures of distinct targets.

Related PDB_ID(s): PDB_ID(s) associated with the same target in TargetDB.

PDB_ID	Title	Target_id	Deposition Date	Released Date	PDB Status	Related PDB_ID in TargetDB
1NNV	the solution structure of hi1450	HI1450	2003-01-14	2004-01-27	REL	none
1NMP	structural genomics, ybgi protein, unknown function	ybgI	2003-01-10	2004-01-20	REL	none
1J9A	oligoribonuclease	HI1715	2001-05-24	2003-06-24	REL	none
1NO5	structure of hi0073 from haemophilus influenzae, the nucleotide binding domain of the hi0073/hi0074 two protein nucleotidyl transferase.	HI0073	2003-01-15	2004-03-16	REL	none
1HTW	complex of hi0065 with adp and magnesium	HI0065	2001-01-01	2002-08-07	REL	none
1NRK	ygfz protein	ygfZ	2003-01-24	2004-03-09	REL	none
1RW1	yffb (pa3664) protein	PA3664	2003-12-15	2004-11-02	REL	none
2OUT	solution structure of hi1506, a novel two domain protein from haemophilus influenzae	HI1506	2007-02-12	2007-05-01	REL	none
1JOP	yhch protein (hi0227)	HI0227	2001-07-30	2003-06-17	REL	none
1K1E	structure of the cobalt-bound form of the deoxy-d-mannose-octulosonate 8-phosphate phosphatase (yrbi) from haemophilus influenzae (hi1679)	HI1679	2001-09-25	2002-02-27	REL	none
3CA8	crystal structure of escherichia coli ydcf, an s-adenosyl-l-methionine utilizing enzyme	ydcF	2008-02-19	2008-05-06	REL	none
2APN	hi1723 solution structure	HI1723	2005-08-16	2006-10-03	REL	none
1J8D	structure of the metal-free form of the deoxy-d-mannose-octulosonate 8-phosphate phosphatase (yrbi) from haemophilus influenzae (hi1679)	HI1679	2001-05-21	2002-02-27	REL	1K1E
1MW5	structure of hi1480 from haemophilus influenzae	HI1480	2002-09-27	2003-11-18	REL	none
1JOS	ribosome binding factor a(rbfa)	HI1288	2001-07-30	2003-06-24	REL	none
1JO0	structure of hi1333, a hypothetical protein from haemophilus influenzae with structural similarity to rna-binding proteins	HI1333	2001-07-26	2002-11-20	REL	none
1MWQ	structure of hi0828, a hypothetical protein from haemophilus influenzae with a putative active-site phosphohistidine	HI0828	2002-09-30	2003-11-25	REL	none
1DBU	crystal structure of cysteinyl-trna(pro) deacylase protein from h. influenzae (hi1434)	HI1434	1999-11-03	2000-06-14	REL	1DBX
1XAX	nmr structure of hi0004, a putative essential gene product from haemophilus influenzae	HI0004	2004-08-26	2005-01-18	REL	none
1NNX	structure of the hypothetical protein ygiw from e. coli.	ygiW	2003-01-14	2004-03-09	REL	none
1M65	ycdx protein	ycdX	2002-07-12	2003-04-22	REL	none
1JJV	dephospho-coa kinase in complex with atp	HI0890	2001-07-09	2002-05-01	REL	none
1JOV	crystal structure analysis of hi1317	HI1317	2001-07-31	2003-06-24	REL	none
1IMU	solution structure of hi0257, a ribosome binding protein	HI0257	2001-05-11	2001-10-03	REL	none
1NMO	structural genomics, protein ybgi, unknown function	ybgI	2003-01-10	2004-01-20	REL	1NMP
1JOE	crystal structure of autoinducer-2 production protein (luxs) from heamophilus influenzae	HI0491	2001-07-27	2001-08-08	REL	none
1MXI	structure of yibk from haemophilus influenzae (hi0766): a methyltransferase with a cofactor bound at a site formed by a knot	HI0766	2002-10-02	2003-02-25	REL	none
1R8G	structure and function of ybdk	ybdK	2003-10-24	2004-08-17	REL	none
1IN0	yajq protein (hi1034)	HI1034	2001-05-11	2003-06-10	REL	none
1NU0	structure of the double mutant (l6m; f134m, semet form) of yqgf from escherichia coli, a hypothetical protein	yqgF	2003-01-30	2004-03-02	REL	none
1J8B	structure of ybab from haemophilus influenzae (hi0442), a protein of unknown function	HI0442	2001-05-21	2003-01-14	REL	none
1MWW	the structure of the hypothetical protein hi1388.1 from haemophilus influenzae reveals a tautomerase/mif fold	HI1388.1	2002-10-01	2003-11-18	REL	none
1DBX	crystal structure of cysteinyl-trna(pro) deacylase from h. influenzae (hi1434)	HI1434	1999-11-03	2000-06-14	REL	none
1FL9	the yjee protein	HI0065	2000-08-13	2002-08-07	REL	1HTW
1J7G	structure of yihz from haemophilus influenzae (hi0670), a d-tyr-trna(tyr) deacylase	HI0670	2001-05-16	2003-04-22	REL	none
1JOG	structure of hi0074 from heamophilus influenzae reveals the fold of a substrate binding domain of a nucleotidyltransferase	HI0074	2001-07-29	2002-12-18	REL	none
2AIZ	solution structure of peptidoglycan associated lipoprotein from haemophilus influenza bound to udp-n-acetylmuramoyl-l-alanyl-d-glutamyl-meso-2,6-diaminopimeloyl-d-alanyl-d-alanine	HI0381	2005-08-01	2006-03-14	REL	none
1X6I	crystal structure of ygfy from escherichia coli	ygfY	2004-08-11	2005-02-08	REL	1X6J
1J85	structure of yibk from haemophilus influenzae (hi0766), a truncated sequence homolog of trna (guanosine-2'-o-) methyltransferase (spou)	HI0766	2001-05-20	2003-02-25	REL	1MXI
1LQA	tas protein from escherichia coli in complex with nadph	b2834	2002-05-09	2003-07-08	REL	none
1RXX	structure of arginine deiminase	PA5171	2003-12-18	2004-01-13	REL	none
1OQF	crystal structure of the 2-methylisocitrate lyase	prpB	2003-03-08	2004-04-27	REL	none
1IM8	crystal structure of yeco from haemophilus influenzae (hi0319), a methyltransferase with a bound s-adenosylhomocysteine	HI0319	2001-05-10	2001-11-07	REL	none
1IZM	structure of ygfb from haemophilus influenzae (hi0817), a conserved hypothetical protein	HI0817	2002-10-09	2003-12-02	REL	none
1X6J	crystal structure of ygfy from escherichia coli	ygfY	2004-08-11	2005-02-08	REL	none
1NMN	structure of yqgf from escherichia coli, a hypothetical protein	yqgF	2003-01-10	2004-03-02	REL	1NU0
1JN1	structure of 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase from haemophilus influenzae (hi0671)	HI0671	2001-07-21	2002-08-21	REL	none
1J7H	solution structure of hi0719, a hypothetical protein from haemophilus influenzae	HI0719	2001-05-16	2003-02-11	REL	none
1JAL	ychf protein (hi0393)	HI0393	2001-05-30	2003-03-25	REL	none
1NIJ	yjia protein	yjiA	2002-12-24	2003-06-24	REL	none
1NNG	structure of hi0827, a thioesterase acting on short-chain acyl-coa compounds.	HI0827	2003-01-13	2004-03-09	Replaced by:1YLI	none

Last updated: Feb 2 2012

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Sequence Redundancy Statistics

Table 5: Sequence Redundancy Statistics for S2F by Experimental Status

Sequence Identity(%)	Novel Targets Status: Selected	Novel Targets Status: Cloned	Novel Targets Status: Expressed	Novel Targets Status: Purified	Novel Targets Status: Crystallized	Novel Targets Status: Crystal Structure	Novel Targets Status: NMR Structure	Novel Targets Status: in PDB
<100	335	309	174	117	45	1	1	44
<98	335	309	174	117	45	1	1	44
<95	335	309	174	117	45	1	1	44
<90	335	309	174	117	45	1	1	44
<70	333	307	172	116	45	1	1	44
<50	318	297	166	113	45	1	1	44
<40	312	292	166	113	45	1	1	44
<30	267	268	157	112	45	1	1	44

Last updated: 12-01-10

Sequence redundancy is calculated by clustering analysis using BLASTClust program with similarity threshold set to percent of sequence identity.   Please view detailed explanation of sequence redundancy calculations and BLASTClust threshold settings.  Sequence redundancy calculations are based on comparison to all protein sequences in TargetDB which are in the same experimental status category and at least 20 amino acids long.

Table 6: Sequence Redundancy Statistics for Structures Released by S2F by Year

Year	Released Structures	Number of Released Structures <30% Identity at Time of Release	Percent(%) of Released Structures <30% Identity(%) at Time of Release
<= 2000	2	1	50
2001	3	2	67
2002	8	3	38
2003	18	11	61
2004	13	8	62
2005	3	1	33
2006	2	0	0
2007	1	1	100
2008	1	1	100
Total	51	28	55

Last updated: 12-02-02

Sequence redundancy is calculated by clustering analysis using BLASTClust program with similarity threshold set to percent of sequence identity.   Please view detailed explanation of sequence redundancy calculations and BLASTClust threshold settings.  Sequence redundancy calculations are based on comparison to all protein sequences in the PDB which are at least 20 amino acids long.

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