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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CHLORIDE-BOUND FORM OF BLUE COPPER NITRITE REDUCTASE
 
Authors :  M. Nojiri
Date :  04 Dec 15  (Deposition) - 23 Nov 16  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Copper Nitrite Reductase, Chloride Ion, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nojiri
Structure And Function Of Copper Nitrite Reductase
Metalloenzymes In 91 2016 Denitrification: Applications And Environmental Impacts
PubMed: search  |  Reference-DOI: 10.1039/9781782623762-00091

(-) Compounds

Molecule 1 - COPPER-CONTAINING NITRITE REDUCTASE
    Chains: A
    EC Number: 1.7.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23C
    Expression System Strain: JM109(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NIR, NIRK, ERS451415_02178
    Organism Common: ACHROMOBACTER XYLOSOXIDANS
    Organism Scientific: ALCALIGENES XYLOSOXYDANS XYLOSOXYDANS
    Organism Taxid: 85698
    Synonym: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE,NITRITE REDUCTASE (NIR)

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CU2Ligand/IonCOPPER (II) ION
3PG42Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CU-1Ligand/IonCOPPER (II) ION
3PG46Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:89 , CYS A:130 , HIS A:139 , MET A:144binding site for residue CU A 401
2AC2SOFTWAREHIS A:94 , HIS A:129 , HIS A:300 , CL A:403 , HOH A:501binding site for residue CU A 402
3AC3SOFTWAREHIS A:129 , ILE A:251 , HIS A:300 , CU A:402 , HOH A:501binding site for residue CL A 403
4AC4SOFTWAREGLU A:133 , MET A:135 , ALA A:194binding site for residue PG4 A 404
5AC5SOFTWAREVAL A:294 , ALA A:296 , PHE A:306 , HIS A:313 , HOH A:721binding site for residue PG4 A 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B1K)

(-) Cis Peptide Bonds  (2, 3)

Asymmetric Unit
No.Residues
1Pro A:16 -Pro A:17
2Met A:62 -Pro A:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B1K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B1K)

(-) Exons   (0, 0)

(no "Exon" information available for 5B1K)

(-) 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    
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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:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b1k A   2 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP 335
                                    11        21        31        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
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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 5B1K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B1K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B1K)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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UniProtKB/TrEMBL
        O68601_ALCXX | O68601: 1bq5 1gs6 1gs7 1gs8 1hau 1haw 1ndt 1oe1 1oe2 1oe3 1wa0 1wa1 1wa2 1wae 2bo0 2bp0 2bp8 2jfc 2vm3 2vm4 2vmj 2vn3 2vw4 2vw6 2vw7 2xwz 2xx0 2xx1 2xxf 2xxg 2zon 4csp 4csz 5b1j

(-) Related Entries Specified in the PDB File

5b1j