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(-) Description

Title :  CRYSTAL STRUCTURE OF NQRF FAD-BINDING DOMAIN FROM VIBRIO CHOLERAE
 
Authors :  G. Fritz
Date :  06 Aug 14  (Deposition) - 03 Dec 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Sodium Translocation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Steuber, G. Vohl, M. S. Casutt, T. Vorburger, K. Diederichs, G. Frit
Structure Of The V. Cholerae Na+-Pumping Nadh:Quinone Oxidoreductase.
Nature V. 516 62 2014
PubMed-ID: 25471880  |  Reference-DOI: 10.1038/NATURE14003

(-) Compounds

Molecule 1 - NA(+)-TRANSLOCATING NADH-QUINONE REDUCTASE SUBUNIT F
    Chains: A, B
    EC Number: 1.6.5.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 130-148
    Gene: NQRF, VC_2290
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Strain: ATCC 39315 / EL TOR INABA N16961
    Synonym: NA(+)-TRANSLOCATING NQR SUBUNIT F,NQR COMPLEX SUBUNIT F,NQR- 1 SUBUNIT F

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3MG2Ligand/IonMAGNESIUM ION
4NA2Ligand/IonSODIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:210 , ALA A:211 , TYR A:212 , SER A:213 , ASN A:227 , VAL A:228 , ARG A:229 , ALA A:231 , THR A:232 , PRO A:233 , PRO A:241 , PRO A:242 , GLY A:243 , GLN A:244 , MET A:245 , SER A:246 , PHE A:406 , HOH A:1635 , HOH A:1672 , HOH A:1675 , HOH A:1690 , HOH A:1702 , HOH A:1742 , HOH A:1755 , HOH A:1792 , GLU B:398 , HOH B:1603binding site for residue FAD A 1501
2AC2SOFTWAREARG A:229 , GLY A:282 , ALA A:283 , GLY A:284 , GLY A:379 , PRO A:380 , HOH A:1746 , HOH A:1819binding site for residue ACT A 1502
3AC3SOFTWARELYS A:143 , TYR A:188 , ARG A:315 , MET A:317 , HOH A:1783 , HOH A:1852binding site for residue MG A 1503
4AC4SOFTWAREALA A:327 , ASN A:330 , PHE A:333 , HOH A:1796 , HOH A:1826binding site for residue NA A 1504
5AC5SOFTWAREHOH A:1604 , ARG B:210 , ALA B:211 , TYR B:212 , SER B:213 , ASN B:227 , VAL B:228 , ARG B:229 , ALA B:231 , THR B:232 , PRO B:233 , VAL B:240 , PRO B:241 , PRO B:242 , GLY B:243 , GLN B:244 , MET B:245 , SER B:246 , PHE B:406 , HOH B:1618 , HOH B:1622 , HOH B:1684 , HOH B:1710 , HOH B:1713 , HOH B:1740 , HOH B:1746 , HOH B:1770binding site for residue FAD B 1501
6AC6SOFTWAREARG B:229 , GLY B:281 , GLY B:282 , ALA B:283 , GLY B:284 , GLY B:379 , PRO B:380 , HOH B:1778binding site for residue ACT B 1502
7AC7SOFTWARELYS B:143 , TYR B:188 , ARG B:315 , MET B:317 , HOH B:1767 , HOH B:1806binding site for residue MG B 1503
8AC8SOFTWAREALA B:327 , ASN B:330 , PHE B:333 , HOH B:1730 , HOH B:1807 , HOH B:1847binding site for residue NA B 1504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U9U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:262 -Pro A:263
2Gly B:262 -Pro B:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U9U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U9U)

(-) Exons   (0, 0)

(no "Exon" information available for 4U9U)

(-) 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:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee..eeeeeee.hhhh........eeeeee..eeee.hhh..hhhhhhhhhhhhhhh.eeee...eeeeee.........eeeeeee.............hhhhhhhhhh....eeeeeeee...........eeeeee..hhhhhhhhhhhhhhh......eeeeeee.hhhhh.hhhhhhhhhhhh..eeeeeee...hhhhh...ee.hhhhhhhhhh.....hhhhheeeee.hhhhhhhhhhhhhhh..hhh.eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u9u A 130 VKKWECTVISNDNKATFIKELKLAIPDGESVPFRAGGYIQIEAPAHHVKYADFDVPEKYRGDWDKFNLFRYESKVDEPIIRAYSMANYPEEFGIIMLNVRIATPPPNNPNVPPGQMSSYIWSLKAGDKCTISGPFGEFFAKDTDAEMVFIGGGAGMAPMRSHIFDQLKRLKSKRKMSYWYGARSKREMFYVEDFDGLAAENDNFVWHCALSDPQPEDNWTGYTGFIHNVLYENYLKDHEAPEDCEYYMCGPPMMNAAVINMLKNLGVEEENILLDDFGG 408
                                   139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399         


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee..eeeeeee.hhhh........eeeeee..eeee.hhh..hhhhhhhhhhhhhhh.eeee...eeeeee.........eeeeeee.............hhhhhhhhh.....eeeeeeee...........eeeeee..hhhhhhhhhhhhhhh......eeeeeee.hhhhh.hhhhhhhhhhhh..eeeeeee...hhhhh...ee.hhhhhhhhhh.....hhhhheeeee.hhhhhhhhhhhhhhh..hhh.eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u9u B 130 VKKWECTVISNDNKATFIKELKLAIPDGESVPFRAGGYIQIEAPAHHVKYADFDVPEKYRGDWDKFNLFRYESKVDEPIIRAYSMANYPEEFGIIMLNVRIATPPPNNPNVPPGQMSSYIWSLKAGDKCTISGPFGEFFAKDTDAEMVFIGGGAGMAPMRSHIFDQLKRLKSKRKMSYWYGARSKREMFYVEDFDGLAAENDNFVWHCALSDPQPEDNWTGYTGFIHNVLYENYLKDHEAPEDCEYYMCGPPMMNAAVINMLKNLGVEEENILLDDFG 407
                                   139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399
   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  (0, 0)

(no "SCOP Domain" information available for 4U9U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U9U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U9U)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        NQRF_VIBCH | Q9X4Q8: 4p6v

(-) Related Entries Specified in the PDB File

4p6v 4P6V IS A PROTEIN COMPLEX CONTAINING THIS ENTRY AS DOMAIN OF AN SUBUNIT