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(-) Description

Title :  ROOM TEMPERATURE STRUCTURE OF COPPER NITRITE REDUCTASE FROM GEOBACILLUS THERMODENITRIFICANS
 
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 :  1.35
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 Strain: BL21(DE3)
    Expression System Taxid: 469008
    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  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2CU12Ligand/IonCOPPER (II) ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2CU-1Ligand/IonCOPPER (II) ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:95 , CYS A:135 , HIS A:143 , MET A:148binding site for residue CU A 401
02AC2SOFTWAREHIS A:100 , HIS A:134 , HIS A:294 , HOH A:504 , HOH A:681binding site for residue CU A 402
03AC3SOFTWAREASP A:55 , HOH A:521 , HOH A:546binding site for residue CU A 403
04AC4SOFTWAREHIS A:39 , HOH A:677binding site for residue CU A 404
05AC5SOFTWAREASP A:167 , ACY A:413 , HOH A:501 , HOH A:503 , HOH A:511 , HOH A:528binding site for residue CU A 405
06AC6SOFTWAREHIS A:42 , GLU A:53 , HIS A:83 , HOH A:605 , HOH A:680binding site for residue CU A 406
07AC7SOFTWAREMET A:270binding site for residue CU A 407
08AC8SOFTWAREILE A:18 , HIS A:21 , TRP A:63 , TYR A:180 , HOH A:683binding site for residue CU A 408
09AC9SOFTWAREPRO A:191 , GLU A:239 , HIS A:298 , CU A:412 , HOH A:671 , HOH A:691binding site for residue CU A 409
10AD1SOFTWAREGLU A:169 , HOH A:558binding site for residue CU A 410
11AD2SOFTWAREASP A:98 , HIS A:100 , HIS A:244 , VAL A:246 , HOH A:504 , HOH A:616binding site for residue CU A 411
12AD3SOFTWAREGLU A:239 , CU A:409 , HOH A:637 , HOH A:649 , HOH A:691binding site for residue CU A 412
13AD4SOFTWAREGLU A:165 , ASP A:167 , CU A:405 , HOH A:501 , HOH A:503 , HOH A:511binding site for residue ACY A 413

(-) SS Bonds  (0, 0)

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

(-) 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 4YSD)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YSD)

(-) 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:299
                                                                                                                                                                                                                                                                                                                                           
               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
                 4ysd A  16 NVIAAHKGVNQAPVPLKMERVGPHDVHIEMTAQITDIEIDKGKIYKAWTFNGQAPGPLVVVNEGDTIHFTLKNMDPVVPHSMDFHAVHASPSKDFIDVMPNKSGTFTYPANKPGVFMYHCGTKPVLQHIANGMHGVIIVKPKNGYPTDKEVDREYVLIQNEWYKYNDMNDFQNGVPSYVVFSSKALKPGDPNTNGDTFTLKEKPLLAKVGEKIRLYINNVGPNEVSSFHVVGTVFDDVYLDGNPNNHLQGMQTVMLPASGGAVVEFTVTRPGTYPIVTHQFNHAQKGAVAMLKVTETGE 314
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305
   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 4YSD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4yso 4ysp 4ysq 4ysr 4yss 4yst 4ysu 4zk8

(-) Related Entries Specified in the PDB File

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