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(-) Description

Title :  THE CRYSTAL STRUCTURE OF NITROREDUCTASE A FROM VIBRIO PARAHAEMOLYTICUS RIMD 2210633
 
Authors :  K. Tan, M. Zhou, W. F. Anderson, A. Joachimiak, Center For Structural Of Infectious Diseases (Csgid)
Date :  16 Feb 17  (Deposition) - 01 Mar 17  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, M. Zhou, W. F. Anderson, A. Joachimiak
The Crystal Structure Of Nitroreductase A From Vibrio Parahaemolyticus Rimd 2210633
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NADPH-FLAVIN OXIDOREDUCTASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG53
    Expression System Strain: BL21(DE3)MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VPA1601
    Organism Taxid: 223926
    Strain: RIMD 2210633

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 37)

Asymmetric Unit (4, 37)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
3GOL1Ligand/IonGLYCEROL
4MSE28Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3GOL-1Ligand/IonGLYCEROL
4MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 17)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3GOL1Ligand/IonGLYCEROL
4MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:11 , SER A:13 , ARG A:15 , GLN A:67 , TYR A:69 , VAL A:127 , TYR A:128 , ILE A:129 , GLY A:130 , GLY A:131 , LYS A:167 , ARG A:169 , HOH A:404 , HOH A:406 , HOH A:441 , HOH A:450 , SER B:38 , SER B:39 , SER B:40 , MSE B:42 , ASP B:107binding site for residue FMN A 301
2AC2SOFTWAREGLY A:130 , ARG A:225 , HOH A:407binding site for residue CL A 302
3AC3SOFTWARESER A:38 , SER A:39 , SER A:40 , MSE A:42 , ASP A:107 , ILE A:110 , HIS B:11 , ARG B:12 , SER B:13 , ARG B:15 , GLN B:67 , TYR B:69 , VAL B:127 , TYR B:128 , ILE B:129 , GLY B:130 , GLY B:131 , LYS B:167 , ARG B:169 , HOH B:403 , HOH B:455 , HOH B:464 , HOH B:471binding site for residue FMN B 301
4AC4SOFTWAREARG B:12 , ILE B:14 , GLU B:120 , GLY B:125 , GLY B:126binding site for residue CL B 302
5AC5SOFTWAREHIS C:11 , ARG C:12 , SER C:13 , ARG C:15 , GLN C:67 , TYR C:69 , VAL C:127 , TYR C:128 , ILE C:129 , GLY C:130 , GLY C:131 , LYS C:167 , ARG C:169 , HOH C:411 , HOH C:459 , HOH C:460 , HOH C:471 , SER D:38 , SER D:39 , SER D:40 , MSE D:42 , ASP D:107binding site for residue FMN C 301
6AC6SOFTWAREGLY C:130 , ARG C:225binding site for residue CL C 302
7AC7SOFTWARESER C:38 , SER C:39 , SER C:40 , ASP C:107 , ILE C:110 , HIS D:11 , ARG D:12 , SER D:13 , ARG D:15 , GLN D:67 , TYR D:69 , VAL D:127 , TYR D:128 , ILE D:129 , GLY D:130 , GLY D:131 , LYS D:167 , ARG D:169 , HOH D:402 , HOH D:433 , HOH D:453 , HOH D:460binding site for residue FMN D 301
8AC8SOFTWAREARG D:12 , ILE D:14 , GLU D:120 , GLY D:123 , LEU D:124 , HOH D:422 , HOH D:431binding site for residue GOL D 302
9AC9SOFTWARESER D:19 , GLN D:20binding site for residue CL D 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5UU6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5UU6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UU6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UU6)

(-) Exons   (0, 0)

(no "Exon" information available for 5UU6)

(-) 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:233
                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeee..hhhhhhhhhhhh...hhhhhh.eeeeeeeehhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....eeeeeeeeee............hhhhheee......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uu6 A   0 AmNSTIQTILGHRSIRKFTSQPIDKEQLETILQAGLAASSSSmLQVVSIVRVTDIEKRSQLAKFAGNQAYVESAAEFLVFCIDYQRHASINPDVQADFTELmLIGAVDSGImAQNCLLAAESmGLGGVYIGGLRNNAQQVDELLGLPQNTAILFGmCLGHPDQNPEVKPRLPAHVVVHENQYQDLNLDDIQAYDQTmQNYYASTWSQEVTSKLAGESRPHILPYLNGKGLAKK 240
                             |       9        19        29        39  |     49        59        69        79        89        99 |     109 |     119  |    129       139       149     | 159       169       179       189      |199 ||    217       227       237   
                             |                                       42-MSE                                                    101-MSE   111-MSE    122-MSE                          155-MSE                                  196-MSE1|                              
                             1-MSE                                                                                                                                                                                                  210                              


Chain B from PDB  Type:PROTEIN  Length:233
                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeee..hhhhhhhhhhhh...hhhhhh.eeeeeeeehhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....eeeeeeeeee............hhhhheee......hhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uu6 B   1 mNSTIQTILGHRSIRKFTSQPIDKEQLETILQAGLAASSSSmLQVVSIVRVTDIEKRSQLAKFAGNQAYVESAAEFLVFCIDYQRHASINPDVQADFTELmLIGAVDSGImAQNCLLAAESmGLGGVYIGGLRNNAQQVDELLGLPQNTAILFGmCLGHPDQNPEVKPRLPAHVVVHENQYQDLNLDDIQAYDQTmQNYYAQSTWSQEVTSKLAGESRPHILPYLNGKGLAKK 240
                            |       10        20        30        40 |      50        60        70        80        90       100|      110|      120 |     130       140       150    |  160       170       180       190     | 200||     217       227       237   
                            1-MSE                                   42-MSE                                                    101-MSE   111-MSE    122-MSE                          155-MSE                                  196-MSE1|                               
                                                                                                                                                                                                                                   209                               


Chain C from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeee..hhhhhhhhhhhh...hhhhhh.eeeeeeeehhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....eeeeeeeeee............hhhhheee......hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uu6 C   0 AmNSTIQTILGHRSIRKFTSQPIDKEQLETILQAGLAASSSSmLQVVSIVRVTDIEKRSQLAKFAGNQAYVESAAEFLVFCIDYQRHASINPDVQADFTELmLIGAVDSGImAQNCLLAAESmGLGGVYIGGLRNNAQQVDELLGLPQNTAILFGmCLGHPDQNPEVKPRLPAHVVVHENQYQDLNLDDIQAYDQTmQNYYANRQSTWSQEVTSKLAGESRPHILPYLNGKGLAKK 240
                             |       9        19        29        39  |     49        59        69        79        89        99 |     109 |     119  |    129       139       149     | 159       169       179       189      |199   ||  214       224       234      
                             1-MSE                                   42-MSE                                                    101-MSE   111-MSE    122-MSE                          155-MSE                                  196-MSE203|                               
                                                                                                                                                                                                                                      209                               


Chain D from PDB  Type:PROTEIN  Length:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeee..hhhhhhhhhhhh...hhhhhh.eeeeeeeehhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....eeeeeeeeee............hhhhheee......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uu6 D   0 AmNSTIQTILGHRSIRKFTSQPIDKEQLETILQAGLAASSSSmLQVVSIVRVTDIEKRSQLAKFAGNQAYVESAAEFLVFCIDYQRHASINPDVQADFTELmLIGAVDSGImAQNCLLAAESmGLGGVYIGGLRNNAQQVDELLGLPQNTAILFGmCLGHPDQNPEVKPRLPAHVVVHENQYQDLNLDDIQAYDQTmQNYYANQSTWSQEVTSKLAGESRPHILPYLNGKGLAKK 240
                             |       9        19        29        39  |     49        59        69        79        89        99 |     109 |     119  |    129       139       149     | 159       169       179       189      |199  ||   215       225       235     
                             1-MSE                                   42-MSE                                                    101-MSE   111-MSE    122-MSE                          155-MSE                                  196-MSE02|                               
                                                                                                                                                                                                                                     209
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5UU6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UU6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UU6)

(-) Gene Ontology  (2, 2)

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