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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE OXIDOREDUCTASE PROTEIN FROM SINORHIZOBIUM MELILOTI 1021 IN COMPLEX WITH NADP
 
Authors :  A. Ghosh, R. Bhoshle, R. Toro, A. Gizzi, B. Hillerich, R. Seidel, S. C. Al York Structural Genomics Research Consortium (Nysgrc)
Date :  23 Apr 12  (Deposition) - 16 May 12  (Release) - 16 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase, Nadp, Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ghosh, R. Bhoshle, R. Toro, A. Gizzi, B. Hillerich, R. Seidel, S. C. Almo
Crystal Structure Of A Putative Oxidoreductase Protein From Sinorhizobium Meliloti 1021 In Complex With Nadp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE OXIDOREDUCTASE
    Chains: A, B, C, D
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: CHS30
    Expression System Strain: BL21(DE3)PRIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: R02322, SMC01571
    Organism Common: ENSIFER MELILOTI
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 266834
    Strain: 1021

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , THR A:16 , HIS A:17 , GLY A:18 , MSE A:19 , GLY A:38 , ARG A:39 , ASN A:40 , ASN A:43 , SER A:60 , ASP A:61 , ILE A:62 , ASN A:88 , ALA A:89 , GLY A:90 , VAL A:111 , THR A:136 , SER A:137 , TYR A:151 , LYS A:155 , PRO A:181 , GLY A:182 , ILE A:184 , THR A:186 , THR A:188 , LYS A:189 , GLY A:190 , HOH A:802 , HOH A:805 , HOH A:810 , HOH A:843 , HOH A:853 , HOH A:859 , HOH A:896BINDING SITE FOR RESIDUE NAP A 700
2AC2SOFTWAREGLY B:14 , THR B:16 , HIS B:17 , MSE B:19 , ARG B:39 , ASN B:40 , ASN B:43 , SER B:60 , ASP B:61 , ILE B:62 , ASN B:88 , ALA B:89 , GLY B:90 , VAL B:111 , THR B:136 , SER B:137 , SER B:138 , TYR B:151 , LYS B:155 , PRO B:181 , GLY B:182 , ILE B:184 , THR B:186 , THR B:188 , LYS B:189 , GLY B:190 , GOL B:701 , HOH B:802 , HOH B:814 , HOH B:834 , HOH B:846BINDING SITE FOR RESIDUE NAP B 700
3AC3SOFTWARESER B:138 , MSE B:148 , PHE B:202 , NAP B:700BINDING SITE FOR RESIDUE GOL B 701
4AC4SOFTWAREGLY C:14 , THR C:16 , HIS C:17 , MSE C:19 , GLY C:38 , ARG C:39 , ASN C:40 , ASN C:43 , SER C:60 , ASP C:61 , ILE C:62 , ASN C:88 , ALA C:89 , GLY C:90 , THR C:136 , SER C:137 , SER C:138 , TYR C:151 , LYS C:155 , GLY C:182 , ILE C:184 , ARG C:199 , GOL C:701 , HOH C:835BINDING SITE FOR RESIDUE NAP C 700
5AC5SOFTWARESER C:92 , NAP C:700BINDING SITE FOR RESIDUE GOL C 701
6AC6SOFTWAREGLY D:14 , THR D:16 , HIS D:17 , MSE D:19 , ARG D:39 , ASN D:40 , ASN D:43 , SER D:60 , ASP D:61 , ILE D:62 , ASN D:88 , ALA D:89 , GLY D:90 , THR D:136 , SER D:137 , SER D:138 , TYR D:151 , LYS D:155 , PRO D:181 , GLY D:182 , ILE D:184 , THR D:186BINDING SITE FOR RESIDUE NAP D 700

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:181 -Gly A:182
2Pro B:181 -Gly B:182
3Thr B:252 -Ala B:253
4Lys C:189 -Gly C:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ESO)

(-) Sequences/Alignments

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:250
                                                                                                                                                                                                                                                                                          
               SCOP domains d4esoa_ A: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.............hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.......eeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eso A   3 GNYQGKKAIVIGGTHGmGLATVRRLVEGGAEVLLTGRNESNIARIREEFGPRVHALRSDIADLNEIAVLGAAAGQTLGAIDLLHINAGVSELEPFDQVSEASYDRQFAVNTKGAFFTVQRLTPLIREGGSIVFTSSVADEGGHPGmSVYSASKAALVSFASVLAAELLPRGIRVNSVSPGFIDTPTKGVAGITEAERAEFKTLGDNITPmKRNGTADEVARAVLFLAFEATFTTGAKLAVDGGLGQKLST 252
                                    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
                                           19-MSE                                                                                                                          148-MSE                                                         212-MSE                                    


Chain B from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains d4esob_ B: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..............hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.......eee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eso B   3 GNYQGKKAIVIGGTHGmGLATVRRLVEGGAEVLLTGRNESNIARIREEFGPRVHALRSDIADLNEIAVLGAAAGQTLGAIDLLHINAGVSELEPFDQVSEASYDRQFAVNTKGAFFTVQRLTPLIREGGSIVFTSSVADEGGHPGmSVYSASKAALVSFASVLAAELLPRGIRVNSVSPGFIDTPTKGVAGITEAERAEFKTLGDNITPmKRNGTADEVARAVLFLAFEATFTTGAKLAVDGGLGQKLSTA 253
                                    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 
                                           19-MSE                                                                                                                          148-MSE                                                         212-MSE                                     


Chain C from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains d4esoc_ C: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.......eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eso C   3 GNYQGKKAIVIGGTHGmGLATVRRLVEGGAEVLLTGRNESNIARIREEFGPRVHALRSDIADLNEIAVLGAAAGQTLGAIDLLHINAGVSELEPFDQVSEASYDRQFAVNTKGAFFTVQRLTPLIREGGSIVFTSSVADEGGHPGmSVYSASKAALVSFASVLAAELLPRGIRVNSVSPGFIDTKGVAGITEAERAEFKTLGDNITPmKRNGTADEVARAVLFLAFEATFTTGAKLAVDGGLGQKLS 251
                                    12      | 22        32        42        52        62        72        82        92       102       112       122       132       142     | 152       162       172       182   ||  194       204       214       224       234       244       
                                           19-MSE                                                                                                                          148-MSE                               186|                    212-MSE                                   
                                                                                                                                                                                                                  189                                                              


Chain D from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains d4esod_ D: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.......hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.......eeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eso D   3 GNYQGKKAIVIGGTHGmGLATVRRLVEGGAEVLLTGRNESNIARIREEFGPRVHALRSDIADLNEIAVLGAAAGQTLGAIDLLHINAGVSELEPFDQVSEASYDRQFAVNTKGAFFTVQRLTPLIREGGSIVFTSSVADEGGHPGmSVYSASKAALVSFASVLAAELLPRGIRVNSVSPGFIDTPTEAERAEFKTLGDNITPmKRNGTADEVARAVLFLAFEATFTTGAKLAVDGGLGQKLS 251
                                    12      | 22        32        42        52        62        72        82        92       102       112       122       132       142     | 152       162       172       182    || 199       209  |    219       229       239       249  
                                           19-MSE                                                                                                                          148-MSE                                187|              212-MSE                                   
                                                                                                                                                                                                                   195
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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    Thr B:252 - Ala B:253   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q92N93_RHIME | Q92N93: 3vc7

(-) Related Entries Specified in the PDB File

3vc7 IN ITS APO STATE RELATED ID: NYSGRC-012068 RELATED DB: TARGETTRACK