1S99 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THE STRUCTURE AND FUNCTION OF B. SUBTILIS YKOF GENE PRODUCT: LIGAND FREE PROTEIN

Authors :   Y. Devedjiev, Y. Surendranath, U. Derewenda, Z. S. Derewenda

Date :   04 Feb 04 (Deposition) - 05 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym./Biol. Unit : A,B

Keywords :   Ykof, Thiamin-Binding Protein, Act-Domain Family, X-Ray Structure, Ligand Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Devedjiev, Y. Surendranath, U. Derewenda, A. Gabrys, D. R. Cooper, R. G. Zhang, L. Lezondra, A. Joachimiak, Z. S. Derewenda
The Structure And Ligand Binding Properties Of The B. Subtilis Ykof Gene Product, A Member Of A Novel Family Of Thiamin/Hmp-Binding Proteins
J. Mol. Biol. V. 343 395 2004
PubMed-ID: 15451668 | Reference-DOI: 10.1016/J.JMB.2004.08.037
(for further references see the PDB file header)

Molecule 1 - YKOF
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	YKOF
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Other Details	:	THIAMIN BINDING PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 17)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CA	1	Ligand/Ion	CALCIUM ION
3	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:15 , SER A:16 , LEU A:17 , SER A:48 , THR A:49	BINDING SITE FOR RESIDUE ACT A 201
2	AC2	SOFTWARE	PHE B:15 , SER B:16 , LEU B:17 , SER B:48 , THR B:49	BINDING SITE FOR RESIDUE ACT B 201
3	AC3	SOFTWARE	ALA A:33 , THR A:35 , HOH A:808 , HOH A:846 , HOH A:990 , ALA B:33 , THR B:35	BINDING SITE FOR RESIDUE CA A 801

(no "SS Bond" information available for 1S99)

(no "Cis Peptide Bond" information available for 1S99)

(no "SAP(SNP)/Variant" information available for 1S99)

(no "PROSITE Motif" information available for 1S99)

(no "Exon" information available for 1S99)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:186
 aligned with YKOF_BACSU | O34911 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:189
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188         
           YKOF_BACSU     9 RIAGFRFSLYPMTDDFISVIKSALKKTDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVMNGTFSIGCPGDTQGDTYLSKGDKRVNEDAVRGLKAEAPCQFALYPMNEPDYMGLIMEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRMAEQQTNHITMTVNLSANSPSRKNR 197
               SCOP domains d1s99a_ A: Putative thiamin/HMP-binding protein YkoF                                                                                                                                          SCOP domains
               CATH domains 1s99A01 A:9-87  [code=3.30.70.930, no name defined]                            ------------------------1s99A02 A:112-197  [code=3.30.70.930, no name defined]                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...hhhhhhhhhhhhh.....eeee....eeeeehhhhhhhhhhhhhhhhhh....eeeeeeeee............---.................eeeeeee....hhhhhhhhhhhhhhhh..eeeee..eeee..hhhhhhhhhhhhhhhhhhhh..eeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s99 A   9 RIAGFRFSLYPmTDDFISVIKSALAATDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVmNGTFSIGCPGDTQGDTYL---DKRVNEDAVRGLKAEAPCQFALYPmNEPDYmGLImEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRmAEQQTNHITmTVNLSANSPSRKNR 197
                                    18 |      28        38        48        58        68        78        88       | - |     108       118     | 128 |   | 138       148       158       168    |  178    |  188         
                                      20-MSE                                                    78-MSE            96 100                     124-MSE |   |                                    173-MSE   183-MSE          
                                                                                                                                                   130-MSE                                                               
                                                                                                                                                       134-MSE

Chain B from PDB  Type:PROTEIN  Length:180
 aligned with YKOF_BACSU | O34911 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:184
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188    
           YKOF_BACSU     9 RIAGFRFSLYPMTDDFISVIKSALKKTDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVMNGTFSIGCPGDTQGDTYLSKGDKRVNEDAVRGLKAEAPCQFALYPMNEPDYMGLIMEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRMAEQQTNHITMTVNLSANSP 192
               SCOP domains d1s99b_ B: Putative thiamin/HMP-binding protein YkoF                                                                                                                                     SCOP domains
               CATH domains 1s99B01 B:9-87  [code=3.30.70.930, no name defined]                            ------------------------1s99B02 B:112-192  [code=3.30.70.930, no name defined]                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...hhhhhhhhhhhhh.....eeee....eeeeehhhhhhhhhhhhhhhhhh....eeeeeeeee...........----.................eeeeeee....hhhhhhhhhhhhhhhh..eeeee..eeee..hhhhhhhhhhhhhhhhhhhh..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s99 B   9 RIAGFRFSLYPmTDDFISVIKSALAATDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVmNGTFSIGCPGDTQGDTY----DKRVNEDAVRGLKAEAPCQFALYPmNEPDYmGLImEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRmAEQQTNHITmTVNLSANSP 192
                                    18 |      28        38        48        58        68        78        88      |  - |     108       118     | 128 |   | 138       148       158       168    |  178    |  188    
                                      20-MSE                                                    78-MSE           95  100                     124-MSE |   |                                    173-MSE   183-MSE     
                                                                                                                                                   130-MSE                                                          
                                                                                                                                                       134-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: MTH1187/YkoF-like (11)

Family: Putative thiamin/HMP-binding protein YkoF (3)

Protein domain: Putative thiamin/HMP-binding protein YkoF (3)

Bacillus subtilis [TaxId: 1423] (3)

1a	d1s99a_	A:
1b	d1s99b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.930, no name defined] (10)

Bacillus subtilis. Organism_taxid: 1423. (2)

1a	1s99A02	A:112-197
1b	1s99B02	B:112-192
1c	1s99A01	A:9-87
1d	1s99B01	B:9-87

(no "Pfam Domain" information available for 1S99)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (YKOF_BACSU | O34911)

molecular function
	GO:0030975	thiamine binding	Interacting selectively and non-covalently with thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
biological process
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1s99)

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	1s99
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	YKOF_BACSU \| O34911	:	1s7h 1sbr

1lxj	X-RAY STRUCTURE OF YBL001C NORTHEAST STRUCTURAL GENOMICS (NESG) CONSORTIUM TARGET YTYST72: SHARES SIMILAR FOLD
1lxn	X-RAY STRUCTURE OF MTH1187 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TT272: SHARES SIMILAR FOLD

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 17)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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