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(-) Description

Title :  COPPER NITRITE REDUCTASE FROM GEOBACILLUS THERMODENITRIFICANS - 0.064 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
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 31-352
    Gene: NIRK, GTNG_0650
    Organism Scientific: GEOBACILLUS THERMODENITRIFICANS (STRAIN NG80- 2)
    Organism Taxid: 420246
    Strain: NG80-2

 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:501 , HOH A:572binding site for residue CU A 402
3AC3SOFTWAREHIS A:42 , GLU A:53 , HIS A:83 , HOH A:554 , HOH A:566binding site for residue CU A 403
4AC4SOFTWAREHIS A:39binding site for residue CU A 404
5AC5SOFTWAREASP A:167 , HOH A:701 , HOH A:726 , HOH A:831 , HOH A:832 , HOH A:854binding site for residue CU A 405
6AC6SOFTWAREHIS A:103 , THR A:248 , VAL A:249 , HOH A:516binding site for residue CU A 406
7AC7SOFTWAREGLU A:239 , HOH A:513 , HOH A:517 , HOH A:521binding site for residue CU A 407
8AC8SOFTWAREASP A:163 , ASP A:167 , ARG A:168 , GLU A:169 , ARG A:229 , HOH A:818 , HOH A:830binding site for residue MPD A 408
9AC9SOFTWAREASP A:55 , THR A:212 , GLN A:300 , HOH A:512binding site for residue SO4 A 409

(-) SS Bonds  (0, 0)

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

(-) 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 4YSO)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YSO)

(-) 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...eeeeee..............hhhhhh.eeee...eeeeeeeeee....eeeee....eeeeee......eeeee..eee....eeeeeee....eeeeeee.hhhhhhh..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yso 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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  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 4YSO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        A4IL26_GEOTN | A4IL26: 3wkp 3wkq 3wni 3wnj 3x1e 3x1f 3x1g 3x1n 4ysa 4ysd 4ysp 4ysq 4ysr 4yss 4yst 4ysu 4zk8

(-) Related Entries Specified in the PDB File

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