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Title :   CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO ALASKENSIS G20 (DDE_0634), TARGET EFI-510102, WITH BOUND D-TRYPTOPHAN

Authors :   M. W. Vetting, N. F. Al Obaidi, L. L. Morisco, S. R. Wasserman, S. Sojitr M. Stead, J. D. Attonito, A. Scott Glenn, S. Chowdhury, B. Evans, B. Hi J. Love, R. D. Seidel, H. J. Imker, J. A. Gerlt, S. C. Almo, Enzyme Funct Initiative (Efi)

Date :   22 Oct 13 (Deposition) - 13 Nov 13 (Release) - 25 Feb 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Trap Periplasmic Solute Binding Family, Enzyme Function Initiative, Efi, Structural Genomics, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. W. Vetting, N. Al-Obaidi, S. Zhao, B. San Francisco, J. Kim, D. J. Wichelecki, J. T. Bouvier, J. O. Solbiati, H. Vu, X. Zhang, D. A. Rodionov, J. D. Love, B. S. Hillerich, R. D. Seidel, R. J. Quinn, A. L. Osterman, J. E. Cronan, M. P. Jacobson, J. A. Gerlt, S. C. Almo
Experimental Strategies For Functional Annotation And Metabolism Discovery: Targeted Screening Of Solute Binding Proteins And Unbiased Panning Of Metabolomes.
Biochemistry V. 54 909 2015
PubMed-ID: 25540822 | Reference-DOI: 10.1021/BI501388Y

Compounds

Molecule 1 - EXTRACELLULAR SOLUTE-BINDING PROTEIN, FAMILY 7
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 30-340
	Gene	:	DDE_0634
	Organism Scientific	:	DESULFOVIBRIO ALASKENSIS
	Organism Taxid	:	207559
	Strain	:	G20

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 68)

Asymmetric Unit (2, 68)

No.	Name	Count	Type	Full Name
1	DTR	4	Ligand/Ion	D-TRYPTOPHAN
2	MSE	64	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 17)

No.	Name	Count	Type	Full Name
1	DTR	1	Ligand/Ion	D-TRYPTOPHAN
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 17)

No.	Name	Count	Type	Full Name
1	DTR	1	Ligand/Ion	D-TRYPTOPHAN
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (2, 17)

No.	Name	Count	Type	Full Name
1	DTR	1	Ligand/Ion	D-TRYPTOPHAN
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (2, 17)

No.	Name	Count	Type	Full Name
1	DTR	1	Ligand/Ion	D-TRYPTOPHAN
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:46 , SER A:97 , TYR A:100 , ARG A:173 , MSE A:194 , THR A:211 , SER A:212 , ASP A:214 , VAL A:215 , TYR A:236 , PHE A:238	BINDING SITE FOR RESIDUE DTR A 401
2	AC2	SOFTWARE	PHE B:46 , SER B:97 , TYR B:100 , ARG B:173 , MSE B:194 , THR B:211 , SER B:212 , ASP B:214 , VAL B:215 , TYR B:236	BINDING SITE FOR RESIDUE DTR B 401
3	AC3	SOFTWARE	PHE C:46 , SER C:97 , TYR C:100 , ARG C:173 , MSE C:194 , THR C:211 , SER C:212 , ASP C:214 , VAL C:215 , TYR C:236 , PHE C:238	BINDING SITE FOR RESIDUE DTR C 401
4	AC4	SOFTWARE	PHE D:46 , SER D:97 , TYR D:100 , ARG D:173 , MSE D:194 , THR D:211 , SER D:212 , ASP D:214 , VAL D:215 , TYR D:236 , PHE D:238	BINDING SITE FOR RESIDUE DTR D 401

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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
	(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:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhh....eeeee.hhh.....hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...eeeee.............eeee.hhhhhhhhhh..eeee.hhhhhhhhhhh....eeee..hhhhhhhhhhh..eeeeeee...eeeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nap A  32 PVTLNYANFPPASTFPCIQmEQWAHEVRTRTRGKVDVLTYPGGTLLGARNmLRGVmSGQADIGCISLAYHPGVFPVmSVFELPLGFTSAEAASSVLWELYSGLRPAELERVKVLTmFTSAPSHFmTVTPVRSLRDLQGmEIRGAGTLSAILEKLGATPVSmPmPEVPEAVQKGIIKGLFTSLDVmKDmNFAEmTGHVTRADQAVYPFAVImNREAWERLSPDVQQVLDGLAAEHAAWTGRYLDAHVQDSmRWAEEKHGVQVHTLPEEDIAAmRRSVQPLFDAWAQRAADKGADPDAVmRTVDALKAQY 339
                                    41        51        61        71        81|    |  91       101      |111       121       131       141     | 151    |  161       171       181       191| |    201       211    |  221  |    231       241|      251       261       271       281       291       301 |     311       321       331        
                                              51-MSE                         82-MSE|                  108-MSE                                147-MSE  156-MSE       170-MSE               192-MSE                 216-MSE   |               242-MSE                                281-MSE               303-MSE                   329-MSE      
                                                                                  87-MSE                                                                                                    194-MSE                  219-MSE|                                                                                                                   
                                                                                                                                                                                                                          224-MSE

Chain B from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhhhhh...eeeeeehhhh.....hhhhhhhh....eeeee.hhh.....hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...eeeee.....hhhhhh..eeee.hhhhhhhhhh..eeee.hhhhhhhhhhh....eeee..hhhhhhhhhhh..eeeeeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nap B  31 QPVTLNYANFPPASTFPCIQmEQWAHEVRTRTRGKVDVLTYPGGTLLGARNmLRGVmSGQADIGCISLAYHPGVFPVmSVFELPLGFTSAEAASSVLWELYSGLRPAELERVKVLTmFTSAPSHFmTVTPVRSLRDLQGmEIRGAGTLSAILEKLGATPVSmPmPEVPEAVQKGIIKGLFTSLDVmKDmNFAEmTGHVTRADQAVYPFAVImNREAWERLSPDVQQVLDGLAAEHAAWTGRYLDAHVQDSmRWAEEKHGVQVHTLPEEDIAAmRRSVQPLFDAWAQRAADKGADPDAVmRTVDALKAQY 339
                                    40        50|       60        70        80 |    | 90       100       110       120       130       140      |150     | 160       170       180       190 | |   200       210     | 220   |   230       240 |     250       260       270       280|      290       300  |    310       320       330         
                                               51-MSE                         82-MSE|                  108-MSE                                147-MSE  156-MSE       170-MSE               192-MSE                 216-MSE   |               242-MSE                                281-MSE               303-MSE                   329-MSE      
                                                                                   87-MSE                                                                                                    194-MSE                  219-MSE|                                                                                                                   
                                                                                                                                                                                                                           224-MSE

Chain C from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhhhh...eeeeeehhhh.....hhhhhhhh....eeeee.hhh.....hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...eeeee.............eeee.hhhhhhhhhhh.eeee.hhhhhhhhhhh....eeee..hhhhhhhhhhh..eeeeeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nap C  32 PVTLNYANFPPASTFPCIQmEQWAHEVRTRTRGKVDVLTYPGGTLLGARNmLRGVmSGQADIGCISLAYHPGVFPVmSVFELPLGFTSAEAASSVLWELYSGLRPAELERVKVLTmFTSAPSHFmTVTPVRSLRDLQGmEIRGAGTLSAILEKLGATPVSmPmPEVPEAVQKGIIKGLFTSLDVmKDmNFAEmTGHVTRADQAVYPFAVImNREAWERLSPDVQQVLDGLAAEHAAWTGRYLDAHVQDSmRWAEEKHGVQVHTLPEEDIAAmRRSVQPLFDAWAQRAADKGADPDAVmRTVDALKAQYG 340
                                    41        51        61        71        81|    |  91       101      |111       121       131       141     | 151    |  161       171       181       191| |    201       211    |  221  |    231       241|      251       261       271       281       291       301 |     311       321       331         
                                              51-MSE                         82-MSE|                  108-MSE                                147-MSE  156-MSE       170-MSE               192-MSE                 216-MSE   |               242-MSE                                281-MSE               303-MSE                   329-MSE       
                                                                                  87-MSE                                                                                                    194-MSE                  219-MSE|                                                                                                                    
                                                                                                                                                                                                                          224-MSE

Chain D from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhhhhhhhh....eeeeehhhh.....hhhhhhhh....eeeee.hhh.....hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeee...eeeee.....hhhhhh..eeee.hhhhhhhhhh..eeee.hhhhhhhhhhh....eeee.hhhhhhhhhhhh..eeeeeee...eeeeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nap D  32 PVTLNYANFPPASTFPCIQmEQWAHEVRTRTRGKVDVLTYPGGTLLGARNmLRGVmSGQADIGCISLAYHPGVFPVmSVFELPLGFTSAEAASSVLWELYSGLRPAELERVKVLTmFTSAPSHFmTVTPVRSLRDLQGmEIRGAGTLSAILEKLGATPVSmPmPEVPEAVQKGIIKGLFTSLDVmKDmNFAEmTGHVTRADQAVYPFAVImNREAWERLSPDVQQVLDGLAAEHAAWTGRYLDAHVQDSmRWAEEKHGVQVHTLPEEDIAAmRRSVQPLFDAWAQRAADKGADPDAVmRTVDALKAQYGG 341
                                    41        51        61        71        81|    |  91       101      |111       121       131       141     | 151    |  161       171       181       191| |    201       211    |  221  |    231       241|      251       261       271       281       291       301 |     311       321       331       341
                                              51-MSE                         82-MSE|                  108-MSE                                147-MSE  156-MSE       170-MSE               192-MSE                 216-MSE   |               242-MSE                                281-MSE               303-MSE                   329-MSE        
                                                                                  87-MSE                                                                                                    194-MSE                  219-MSE|                                                                                                                     
                                                                                                                                                                                                                          224-MSE

Legend:		→ Mismatch	(orange background)
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	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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

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