2O1M - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE PROBABLE AMINO-ACID ABC TRANSPORTER EXTRACELLULAR-BINDING PROTEIN YTMK FROM BACILLUS SUBTILIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR572

Authors :   A. P. Kuzin, M. Su, J. Seetharaman, C. X. Chen, Y. Fang, K. Cunningham, L. C. Ma, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. Montelione L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)

Date :   29 Nov 06 (Deposition) - 19 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Nesg X-Ray O34852 Ytmk_bacsu, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. P. Kuzin, M. Su, J. Seetharaman, C. Chen, Y. Fang, K. Cunningham, L. C. Ma, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt
Crystal Structure Of The Probable Amino-Acid Abc Transporter Extracellular-Binding Protein Ytmk From Bacillus Subtilis. Northeast Structural Genomics Consortium Target Sr572.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROBABLE AMINO-ACID ABC TRANSPORTER EXTRACELLULAR-BINDING PROTEIN YTMK
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21
	Expression System Strain	:	BL21(DE3)+MAGIC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YTMK
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:69 , ARG A:90	BINDING SITE FOR RESIDUE SO4 A 401
2	AC2	SOFTWARE	SER B:87 , LYS B:88	BINDING SITE FOR RESIDUE SO4 B 402
3	AC3	SOFTWARE	LYS A:107 , PRO A:179 , THR A:195 , VAL A:196 , GLY A:197 , ASP A:244 , HOH A:425 , HOH A:431 , HOH A:445 , HOH A:455 , HOH A:475	BINDING SITE FOR RESIDUE SO4 A 403
4	AC4	SOFTWARE	SER A:87 , LYS A:88	BINDING SITE FOR RESIDUE SO4 A 404

(no "SS Bond" information available for 2O1M)

(no "Cis Peptide Bond" information available for 2O1M)

(no "SAP(SNP)/Variant" information available for 2O1M)

(no "PROSITE Motif" information available for 2O1M)

(no "Exon" information available for 2O1M)

Asymmetric 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
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Chain A from PDB  Type:PROTEIN  Length:232
 aligned with TCYK_BACSU | O34852 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:232
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263  
           TCYK_BACSU    34 KVQTITVGTGTQFPNICFIDEKGDLTGYDVELIKELDKRLPHYKFTFKTMEFSNLLVSLGQHKVDIVAHQMEKSKEREKKFLFNKVAYNHFPLKITVLQNNDTIRGIEDLKGKRVITSATSNGALVLKKWNEDNGRPFEIAYEGQGANETANQLKSGRADATISTPFAVDFQNKTSTIKEKTVGNVLSNAKVYFMFNKNEQTLSDDIDKALQEIIDDGTLKRLSLKWLGDDY 265
               SCOP domains d2o1ma_ A: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains 2o1mA01 A:14-85,A:207-245 Periplasmic binding protein-like II           2o1mA02 A:86-206 Periplasmic binding protein-like II                                                                     2o1mA01 A:14-85,A:207-245               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..ee...eee.....eehhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh....eeeeee..hhhhhhhhee.....eeeeeeeeee.......hhhhh...eeee...hhhhhhhhhhhhhh....eeee.....hhhhhhhhhh....eeehhhhhhhhhhhh...eeeeeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o1m A  14 KVQTITVGTGTQFPNICFIDEKGDLTGYDVELIKELDKRLPHYKFTFKTmEFSNLLVSLGQHKVDIVAHQmEKSKEREKKFLFNKVAYNHFPLKITVLQNNDTIRGIEDLKGKRVITSATSNGALVLKKWNEDNGRPFEIAYEGQGANETANQLKSGRADATISTPFAVDFQNKTSTIKEKTVGNVLSNAKVYFmFNKNEQTLSDDIDKALQEIIDDGTLKRLSLKWLGDDY 245
                                    23        33        43        53        63        73        83|       93       103       113       123       133       143       153       163       173       183       193       203    |  213       223       233       243  
                                                                            63-MSE               84-MSE                                                                                                                     208-MSE

Chain B from PDB  Type:PROTEIN  Length:224
 aligned with TCYK_BACSU | O34852 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:230
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
           TCYK_BACSU    34 KVQTITVGTGTQFPNICFIDEKGDLTGYDVELIKELDKRLPHYKFTFKTMEFSNLLVSLGQHKVDIVAHQMEKSKEREKKFLFNKVAYNHFPLKITVLQNNDTIRGIEDLKGKRVITSATSNGALVLKKWNEDNGRPFEIAYEGQGANETANQLKSGRADATISTPFAVDFQNKTSTIKEKTVGNVLSNAKVYFMFNKNEQTLSDDIDKALQEIIDDGTLKRLSLKWLGD 263
               SCOP domains d2o1mb_ B: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains 2o1mB01 B:14-85,B:207-243 Periplasmic binding protein-like II           2o1mB02 B:86-206 Periplasmic binding protein-li   ke II                                                                  2o1mB01 B:14-85,B:207-243             CATH domains
           Pfam domains (1) ----SBP_bac_3-2o1mB01 B:18-243                                                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) ----SBP_bac_3-2o1mB02 B:18-243                                                                                                                                                                                                         Pfam domains (2)
         Sec.struct. author ..eeeeeee..ee...eee.....eehhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh..ee......hhhhhhhhee.....eeeeeeeeee.......hhhhh...eee...---hhhhhhhhhh......eee..---.hhhhhhhhhh...eeeehhhhhhhhhhhh...eeeeeeeeeeeee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o1m B  14 KVQTITVGTGTQFPNICFIDEKGDLTGYDVELIKELDKRLPHYKFTFKTmEFSNLLVSLGQHKVDIVAHQmEKSKEREKKFLFNKVAYNHFPLKITVLQNNDTIRGIEDLKGKRVITSA---GALVLKKWNEDNGRPFEIAYE---ANETANQLKSGRADATISTPFAVDFQNKTSTIKEKTVGNVLSNAKVYFmFNKNEQTLSDDIDKALQEIIDDGTLKRLSLKWLGD 243
                                    23        33        43        53        63        73        83|       93       103       113       123        |-  |    143       153  |   |163       173       183       193       203    |  213       223       233       243
                                                                            63-MSE               84-MSE                                         132 136                 156 160                                             208-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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: automated matches (267)

Protein domain: automated matches (267)

Bacillus subtilis [TaxId: 1423] (7)

1a	d2o1ma_	A:
1b	d2o1mb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: D-Maltodextrin-Binding Protein; domain 2 (600)

Homologous Superfamily: Periplasmic binding protein-like II (486)

Bacillus subtilis. Organism_taxid: 1423. (4)

1a	2o1mA02	A:86-206
1b	2o1mB02	B:86-206
1c	2o1mA01	A:14-85,A:207-245
1d	2o1mB01	B:14-85,B:207-243

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

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Clan: PBP (391)

Family: SBP_bac_3 (32)

Bacillus subtilis (1)

1a	SBP_bac_3-2o1mB01	B:18-243
1b	SBP_bac_3-2o1mB02	B:18-243

Asymmetric Unit(hide GO term definitions)

Chain A,B (TCYK_BACSU | O34852)

biological process
	GO:0006865	amino acid transport	The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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