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(-) Description

Title :  STRUCTURE OF COPPER NITRITE REDUCTASE FROM GEOBACILLUS THERMODENITRIFICANS - 8.38 MGY
 
Authors :  Y. Fukuda, K. M. Tse, M. Suzuki, K. Diederichs, K. Hirata, T. Nakane, M. S E. Nango, K. Tono, Y. Joti, T. Kameshima, C. Song, T. Hatsui, M. Yabashi O. Nureki, H. Matsumura, T. Inoue, S. Iwata, E. Mizohata
Date :  17 Mar 15  (Deposition) - 24 Feb 16  (Release) - 25 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Nitrite, Copper, Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Fukuda, K. M. Tse, M. Suzuki, K. Diederichs, K. Hirata, T. Nakane, M. Sugahara, E. Nango, K. Tono, Y. Joti, T. Kameshima, C. Song, T. Hatsui, M. Yabashi, O. Nureki, H. Matsumura, T. Inoue, S. Iwata, E. Mizohata
Redox-Coupled Structural Changes In Nitrite Reductase Revealed By Serial Femtosecond And Microfocus Crystallography
J. Biochem. V. 159 527 2016
PubMed-ID: 26769972  |  Reference-DOI: 10.1093/JB/MVV133

(-) Compounds

Molecule 1 - NITRITE REDUCTASE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 31-352
    GeneNIRK, GTNG_0650
    Organism ScientificGEOBACILLUS THERMODENITRIFICANS (STRAIN NG80- 2)
    Organism Taxid420246
    StrainNG80-2

 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, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CU7Ligand/IonCOPPER (II) ION
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3SO43Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:95 , CYS A:135 , HIS A:143 , MET A:148binding site for residue CU A 401
2AC2SOFTWAREHIS A:100 , HIS A:134 , HIS A:294 , HOH A:740binding site for residue CU A 402
3AC3SOFTWAREHIS A:42 , GLU A:53 , HIS A:83 , HOH A:743binding site for residue CU A 403
4AC4SOFTWAREHIS A:39binding site for residue CU A 404
5AC5SOFTWAREASP A:167 , HOH A:502 , HOH A:650 , HOH A:655 , HOH A:739binding site for residue CU A 405
6AC6SOFTWAREPRO A:191 , GLU A:239 , HOH A:599 , HOH A:633binding site for residue CU A 406
7AC7SOFTWAREHIS A:103 , THR A:248 , VAL A:249 , HOH A:570binding site for residue CU A 407
8AC8SOFTWAREASP A:163 , ASP A:167 , ARG A:168 , GLU A:169 , ARG A:229 , HOH A:504 , HOH A:506binding site for residue MPD A 408
9AC9SOFTWARETYR A:193 , GLN A:300 , LYS A:301 , HOH A:620binding site for residue SO4 A 409

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 4)

Asymmetric Unit
No.Residues
1Ala A:69 -Pro A:70
2Lys A:138 -Pro A:139
3Gly A:236 -Pro A:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YSQ)

(-) 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:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.........eeeeee..eeeeeeeeeeeeeeee..eeeeeeee........eeee..eeeeeeeee.........ee.....hhhhhh.......eeeeeeee...eeeeee....hhhhhhhh..eeeeeee......hhhhh.eeeeeeeeee....hhhhhhhh...eeeeeee.............hhhhhh.eeee...eeeeeeeeee....eeeee....eeeeee......eeeee..eee....eeeeeee....eeeeeee.hhhhhhh..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ysq A  18 IAAHKGVNQAPVPLKMERVGPHDVHIEMTAQITDIEIDKGKIYKAWTFNGQAPGPLVVVNEGDTIHFTLKNMDPVVPHSMDFHAVHASPSKDFIDVMPNKSGTFTYPANKPGVFMYHCGTKPVLQHIANGMHGVIIVKPKNGYPTDKEVDREYVLIQNEWYKYNDMNDFQNGVPSYVVFSSKALKPGDPNTNGDTFTLKEKPLLAKVGEKIRLYINNVGPNEVSSFHVVGTVFDDVYLDGNPNNHLQGMQTVMLPASGGAVVEFTVTRPGTYPIVTHQFNHAQKGAVAMLKVTET 312
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307     

   Legend:   → Mismatch (orange background)
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  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 4YSQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:69 - Pro A:70   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        A4IL26_GEOTN | A4IL263wkp 3wkq 3wni 3wnj 3x1e 3x1f 3x1g 3x1n 4ysa 4ysd 4yso 4ysp 4ysr 4yss 4yst 4ysu 4zk8

(-) Related Entries Specified in the PDB File

4ysa 4ysc 4ysd 4yse 4yso 4ysp 4ysq 4yss 4yst 4ysu