4DA9 - JenaLib

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Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE FROM SINORHIZOBIUM MELILOTI 1021

Authors :   V. N. Malashkevich, R. Bhosle, R. Toro, R. Seidel, S. C. Almo, New York Structural Genomics Research Consortium (Nysgrc)

Date :   12 Jan 12 (Deposition) - 25 Jan 12 (Release) - 02 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A,D  (1x)
Biol. Unit 3: A,C  (1x)
Biol. Unit 4: B,C  (1x)
Biol. Unit 5: B,D  (1x)

Keywords :   Structural Genomics, Protein Structure Initiative, Dehydrogenase/Reductase, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. N. Malashkevich, R. Bhosle, R. Toro, R. Seidel, S. C. Almo
Crystal Structure Of Putative Short-Chain Dehydrogenase/Reductase From Sinorhizobium Meliloti 1021
To Be Published
PubMed: search

Molecule 1 - SHORT-CHAIN DEHYDROGENASE/REDUCTASE
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.100
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BC-PSGX3(BC)
	Expression System Strain	:	BL21(DE3)CODON+RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	R03296, SMC04391
	Organism Scientific	:	SINORHIZOBIUM MELILOTI
	Organism Taxid	:	266834
	Strain	:	1021

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:	A			D
Biological Unit 3 (1x)	:	A		C
Biological Unit 4 (1x)	:		B	C
Biological Unit 5 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 17)

No.	Name	Count	Type	Full Name
1	MSE	13	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 17)

No.	Name	Count	Type	Full Name
1	MSE	13	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 9)

No.	Name	Count	Type	Full Name
1	MSE	7	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 10)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 8)

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

Biological Unit 5 (2, 7)

No.	Name	Count	Type	Full Name
1	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:15 , ARG A:16 , GLY A:37 , ILE A:38 , GLY A:39 , HOH A:407	BINDING SITE FOR RESIDUE SO4 A 301
2	AC2	SOFTWARE	ARG B:15 , ARG B:16 , GLY B:37 , ILE B:38 , GLY B:39 , HOH B:405 , HOH B:426	BINDING SITE FOR RESIDUE SO4 B 301
3	AC3	SOFTWARE	ARG C:15 , ARG C:16 , GLY C:37 , ILE C:38 , GLY C:39	BINDING SITE FOR RESIDUE SO4 C 301
4	AC4	SOFTWARE	ARG D:15 , ARG D:16 , GLY D:37 , ILE D:38 , GLY D:39 , HOH D:403	BINDING SITE FOR RESIDUE SO4 D 301

(no "SS Bond" information available for 4DA9)

(no "Cis Peptide Bond" information available for 4DA9)

(no "SAP(SNP)/Variant" information available for 4DA9)

(no "PROSITE Motif" information available for 4DA9)

(no "Exon" information available for 4DA9)

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:219
 aligned with Q92L02_RHIME | Q92L02 from UniProtKB/TrEMBL  Length:257

    Alignment length:254
                             1                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    
         Q92L02_RHIME     - -MTQKARPVAIVTGGRRGIGLGIARALAASGFDIAITGIGDAEGVAPVIAELSGLGARVIFLRADLADLSSHQATVDAVVAEFGRIDCLVNNAGIASIVRDDFLDLKPENFDTIVGVNLRGTVFFTQAVLKAMLASDARASRSIINITSVSAVMTSPERLDYCMSKAGLAAFSQGLALRLAETGIAVFEVRPGIIRSDMTAAVSGKYDGLIESGLVPMRRWGEPEDIGNIVAGLAGGQFGFATGSVIQADGGLS 253
               SCOP domains d4da9a_ A: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeeee..------.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....eeeeee...-------.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....----------------------...hhhhhhhhhhhhhh..hhhhh..eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4da9 A   0 mmTQKARPVAIVTGGRRGIGLGIARALAASGFDIAITGIGDAEGVAPVIAELSGLGARVIFLRADLADLSSHQATVDAVVAEFGRIDCLVNNAG------DDFLDLKPENFDTIVGVNLRGTVFFTQAVLKAmLASDARASRSIINITSV-------ERLDYCmSKAGLAAFSQGLALRLAETGIAVFEVRPGIIRS----------------------RWGEPEDIGNIVAGLAGGQFGFATGSVIQADGGLS 253
                            ||       9        19        29        39        49        59        69        79        89   |     -|      109       119       129  |    139       149       159   |   169       179       189      |  -         -       219       229       239       249    
                            ||                                                                                          93    100                             132-MSE          149     157     |                              196                    219                                  
                            0-MSE                                                                                                                                                            163-MSE                                                                                      
                             1-MSE

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with Q92L02_RHIME | Q92L02 from UniProtKB/TrEMBL  Length:257

    Alignment length:254
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252    
         Q92L02_RHIME     3 QKARPVAIVTGGRRGIGLGIARALAASGFDIAITGIGDAEGVAPVIAELSGLGARVIFLRADLADLSSHQATVDAVVAEFGRIDCLVNNAGIASIVRDDFLDLKPENFDTIVGVNLRGTVFFTQAVLKAMLASDARASRSIINITSVSAVMTSPERLDYCMSKAGLAAFSQGLALRLAETGIAVFEVRPGIIRSDMTAAVSGKYDGLIESGLVPMRRWGEPEDIGNIVAGLAGGQFGFATGSVIQADGGLSIGR 256
               SCOP domains d4da9b_ B: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee....-----.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....eeeeee...-------.hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee..--------------------------..hhhhhhhhhhhhhh..hhhhh..eeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4da9 B   3 QKARPVAIVTGGRRGIGLGIARALAASGFDIAITGIGDAEGVAPVIAELSGLGARVIFLRADLADLSSHQATVDAVVAEFGRIDCLVNNAGI-----DDFLDLKPENFDTIVGVNLRGTVFFTQAVLKAmLASDARASRSIINITSV-------ERLDYCmSKAGLAAFSQGLALRLAETGIAVFEVRPGI--------------------------WGEPEDIGNIVAGLAGGQFGFATGSVIQADGGLSIGR 256
                                    12        22        32        42        52        62        72        82        92 |     102       112       122       132       142      |  -    |  162|      172       182       192|        -         -       222       232       242       252    
                                                                                                                      94   100                             132-MSE          149     157     |                           193                        220                                    
                                                                                                                                                                                          163-MSE

Chain C from PDB  Type:PROTEIN  Length:220
 aligned with Q92L02_RHIME | Q92L02 from UniProtKB/TrEMBL  Length:257

    Alignment length:254
                             1                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    
         Q92L02_RHIME     - -MTQKARPVAIVTGGRRGIGLGIARALAASGFDIAITGIGDAEGVAPVIAELSGLGARVIFLRADLADLSSHQATVDAVVAEFGRIDCLVNNAGIASIVRDDFLDLKPENFDTIVGVNLRGTVFFTQAVLKAMLASDARASRSIINITSVSAVMTSPERLDYCMSKAGLAAFSQGLALRLAETGIAVFEVRPGIIRSDMTAAVSGKYDGLIESGLVPMRRWGEPEDIGNIVAGLAGGQFGFATGSVIQADGGLS 253
               SCOP domains d4da9c_ C: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeeee..-----..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......eeeeee...-------.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....----------------------...hhhhhhhhhhhhhh..hhhhh..eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4da9 C   0 mmTQKARPVAIVTGGRRGIGLGIARALAASGFDIAITGIGDAEGVAPVIAELSGLGARVIFLRADLADLSSHQATVDAVVAEFGRIDCLVNNAG-----RDDFLDLKPENFDTIVGVNLRGTVFFTQAVLKAmLASDARASRSIINITSV-------ERLDYCmSKAGLAAFSQGLALRLAETGIAVFEVRPGIIRS----------------------RWGEPEDIGNIVAGLAGGQFGFATGSVIQADGGLS 253
                            ||       9        19        29        39        49        59        69        79        89   |    99       109       119       129  |    139       149       159   |   169       179       189      |  -         -       219       229       239       249    
                            0-MSE                                                                                       93    99                              132-MSE          149     157     |                              196                    219                                  
                             1-MSE                                                                                                                                                           163-MSE

Chain D from PDB  Type:PROTEIN  Length:219
 aligned with Q92L02_RHIME | Q92L02 from UniProtKB/TrEMBL  Length:257

    Alignment length:254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250    
         Q92L02_RHIME     1 MTQKARPVAIVTGGRRGIGLGIARALAASGFDIAITGIGDAEGVAPVIAELSGLGARVIFLRADLADLSSHQATVDAVVAEFGRIDCLVNNAGIASIVRDDFLDLKPENFDTIVGVNLRGTVFFTQAVLKAMLASDARASRSIINITSVSAVMTSPERLDYCMSKAGLAAFSQGLALRLAETGIAVFEVRPGIIRSDMTAAVSGKYDGLIESGLVPMRRWGEPEDIGNIVAGLAGGQFGFATGSVIQADGGLSI 254
               SCOP domains d4da9d_ D: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeeee.-------.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....eeeeee...------..hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....----------------------...hhhhhhhhhhhhhh..hhhhh..eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4da9 D   1 mTQKARPVAIVTGGRRGIGLGIARALAASGFDIAITGIGDAEGVAPVIAELSGLGARVIFLRADLADLSSHQATVDAVVAEFGRIDCLVNNA-------DDFLDLKPENFDTIVGVNLRGTVFFTQAVLKAmLASDARASRSIINITSV------PERLDYCmSKAGLAAFSQGLALRLAETGIAVFEVRPGIIRS----------------------RWGEPEDIGNIVAGLAGGQFGFATGSVIQADGGLSI 254
                            |       10        20        30        40        50        60        70        80        90 |     100       110       120       130 |     140        |-     | 160  |    170       180       190     |   -         -       220       230       240       250    
                            1-MSE                                                                                     92     100                             132-MSE          149    156      |                              196                    219                                   
                                                                                                                                                                                            163-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(

)

Folds(

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Superfamilies( (-)

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Families(

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

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: automated matches (447)

Protein domain: automated matches (447)

Sinorhizobium meliloti [TaxId: 266834] (11)

1a	d4da9a_	A:
1b	d4da9b_	B:
1c	d4da9c_	C:
1d	d4da9d_	D:

(no "CATH Domain" information available for 4DA9)

(no "Pfam Domain" information available for 4DA9)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q92L02_RHIME | Q92L02)

molecular function
	GO:0004316	3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity	Catalysis of the reaction: (3R)-3-hydroxyacyl-[acyl-carrier protein] + NADP+ = 3-oxoacyl-[acyl-carrier protein] + NADPH + H+.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Asymmetric Unit
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