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(-) Description

Title :  REDUCED CRYSTAL STRUCTURE OF THE NITROSOMONAS EUROPAEA COPPER NITRITE REDUCTASE AT PH 6.5
 
Authors :  A. C. Rosenzweig, T. L. Lawton, L. A. Sayavedra-Soto, D. J. Arp
Date :  10 May 13  (Deposition) - 24 Jul 13  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,F  (1x)
Biol. Unit 2:  C,D,E  (1x)
Keywords :  Nitrite Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. J. Lawton, K. E. Bowen, L. A. Sayavedra-Soto, D. J. Arp, A. C. Rosenzweig
Characterization Of A Nitrite Reductase Involved In Nitrifier Denitrification.
J. Biol. Chem. V. 288 25575 2013
PubMed-ID: 23857587  |  Reference-DOI: 10.1074/JBC.M113.484543

(-) Compounds

Molecule 1 - MULTICOPPER OXIDASE TYPE 1
    Chains: A, B, C, D, E, F
    Engineered: YES
    Gene: ANIA, NE0924
    Organism Scientific: NITROSOMONAS EUROPAEA
    Organism Taxid: 228410
    Strain: ATCC 19718 / NBRC 14298

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB   F
Biological Unit 2 (1x):   CDE 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2CU12Ligand/IonCOPPER (II) ION
3GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CU-1Ligand/IonCOPPER (II) ION
3GOL2Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CU-1Ligand/IonCOPPER (II) ION
3GOL-1Ligand/IonGLYCEROL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:83 , CYS A:123 , HIS A:131 , MET A:136BINDING SITE FOR RESIDUE CU A 401
02AC2SOFTWAREHIS A:88 , HIS A:122 , HIS F:277BINDING SITE FOR RESIDUE CU A 402
03AC3SOFTWAREHIS B:83 , CYS B:123 , HIS B:131 , MET B:136BINDING SITE FOR RESIDUE CU B 401
04AC4SOFTWAREHIS A:277 , HIS B:88 , HIS B:122BINDING SITE FOR RESIDUE CU B 402
05AC5SOFTWAREARG B:62BINDING SITE FOR RESIDUE CL B 403
06AC6SOFTWAREVAL B:60 , ARG B:309BINDING SITE FOR RESIDUE CL B 404
07AC7SOFTWARETRP A:179 , ARG A:280 , MET B:175 , GLN B:176BINDING SITE FOR RESIDUE GOL B 405
08AC8SOFTWAREHIS C:83 , CYS C:123 , HIS C:131 , MET C:136BINDING SITE FOR RESIDUE CU C 401
09AC9SOFTWAREHIS C:88 , HIS C:122 , HIS E:277BINDING SITE FOR RESIDUE CU C 402
10BC1SOFTWAREVAL C:60 , ARG C:309BINDING SITE FOR RESIDUE CL C 403
11BC2SOFTWAREHIS D:83 , CYS D:123 , HIS D:131 , MET D:136BINDING SITE FOR RESIDUE CU D 401
12BC3SOFTWAREHIS C:277 , ASP D:86 , HIS D:88 , HIS D:122BINDING SITE FOR RESIDUE CU D 402
13BC4SOFTWAREHIS E:83 , CYS E:123 , HIS E:131 , MET E:136BINDING SITE FOR RESIDUE CU E 401
14BC5SOFTWAREHIS D:277 , HIS E:88 , HIS E:122BINDING SITE FOR RESIDUE CU E 402
15BC6SOFTWAREVAL E:60 , ARG E:309BINDING SITE FOR RESIDUE CL E 403
16BC7SOFTWAREHIS F:83 , CYS F:123 , HIS F:131 , MET F:136BINDING SITE FOR RESIDUE CU F 401
17BC8SOFTWAREHIS B:277 , HIS F:88 , HIS F:122BINDING SITE FOR RESIDUE CU F 402
18BC9SOFTWAREGLN A:176 , LYS F:178 , TRP F:179 , ARG F:280BINDING SITE FOR RESIDUE GOL F 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (18, 18)

Asymmetric Unit
No.Residues
1Val A:56 -Pro A:57
2Asp A:126 -Pro A:127
3Gly A:219 -Pro A:220
4Val B:56 -Pro B:57
5Asp B:126 -Pro B:127
6Gly B:219 -Pro B:220
7Val C:56 -Pro C:57
8Asp C:126 -Pro C:127
9Gly C:219 -Pro C:220
10Val D:56 -Pro D:57
11Asp D:126 -Pro D:127
12Gly D:219 -Pro D:220
13Val E:56 -Pro E:57
14Asp E:126 -Pro E:127
15Gly E:219 -Pro E:220
16Val F:56 -Pro F:57
17Asp F:126 -Pro F:127
18Gly F:219 -Pro F:220

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KNS)

(-) 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:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4knsa1 A:25-153 automated matches                                                                                               d4knsa2 A:154-309 automated matches                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee.....hhhhhh.......eeeeeee....eeeeee....hhhhhhhh..eeeeeee...........eeeeeeeeee.....hhhhhhh....eeee..................eee.....eeeeeeeee....eeeeee...eeeeee.hhhhhheeee..eee...eeeeeee.....eeeeeee.hhhhhhhh.eeeeee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kns A  25 KTVQVTLHAVETDVAYDNKGSTYRAWTFDGKVPGPVVRVTEGDTVEFTLINDKNSKNSHSMDFHAARLDVVEDFESIKPGETKKYTFTADNPGVFFYHCGSDPMIQHIARGMYGVIIVDPKDANALPKADREYVLIQAEHYENPDDKTAMMQNKWSNVVFNGGVFKYDPVHDSEATSWLQAKPGERVRIYFVNAGPNELSSLHPIAGIWDRVYPSGNPKNVQYALQSYLIGAGDAATLDLISPVEGANAIVDHSMRHAHSGAIAVIMFTNDADPEAGRGENILIR 309
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304     


Chain B from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4knsb1 B:25-153 automated matches                                                                                               d4knsb2 B:154-309 automated matches                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee..................eeeeeee....eeeeee....hhhhhhhh..eeeeeee...........eeeeeeeeee.....hhhhhhh....eeee..................eee.....eeeeeeeee....eeeeee...eeeeee.hhhhhheeee..eee...eeeeeee.....eeeeeee.hhhhhhh..eeeeee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kns B  25 KTVQVTLHAVETDVAYDNKGSTYRAWTFDGKVPGPVVRVTEGDTVEFTLINDKNSKNSHSMDFHAARLDVVEDFESIKPGETKKYTFTADNPGVFFYHCGSDPMIQHIARGMYGVIIVDPKDANALPKADREYVLIQAEHYENPDDKTAMMQNKWSNVVFNGGVFKYDPVHDSEATSWLQAKPGERVRIYFVNAGPNELSSLHPIAGIWDRVYPSGNPKNVQYALQSYLIGAGDAATLDLISPVEGANAIVDHSMRHAHSGAIAVIMFTNDADPEAGRGENILIR 309
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304     


Chain C from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4knsc1 C:25-153 automated matches                                                                                               d4knsc2 C:154-309 automated matches                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee..................eeeeeee....eeeeee....hhhhhhhh..eeeeeee...........eeeeeeeeee.....hhhhhhh....eeee..................eee.....eeeeeeeee....eeeeee...eeeeee.hhhhhheeee..eee...eeeeeee.....eeeeeee.hhhhhhh..eeeeee.........hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kns C  25 KTVQVTLHAVETDVAYDNKGSTYRAWTFDGKVPGPVVRVTEGDTVEFTLINDKNSKNSHSMDFHAARLDVVEDFESIKPGETKKYTFTADNPGVFFYHCGSDPMIQHIARGMYGVIIVDPKDANALPKADREYVLIQAEHYENPDDKTAMMQNKWSNVVFNGGVFKYDPVHDSEATSWLQAKPGERVRIYFVNAGPNELSSLHPIAGIWDRVYPSGNPKNVQYALQSYLIGAGDAATLDLISPVEGANAIVDHSMRHAHSGAIAVIMFTNDADPEAGRGENILIR 309
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304     


Chain D from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4knsd1 D:25-153 automated matches                                                                                               d4knsd2 D:154-309 automated matches                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee..................eeeeeee....eeeeee....hhhhhhhhh.eeeeeee...........eeeeeeeeee.....hhhhhhh....eeee..................eee.....eeeeeeeee....eeeeee...eeeeee.hhhhhheeee..eee...eeeeeee.....eeeeeee.hhhhhhh..eeeeee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kns D  25 KTVQVTLHAVETDVAYDNKGSTYRAWTFDGKVPGPVVRVTEGDTVEFTLINDKNSKNSHSMDFHAARLDVVEDFESIKPGETKKYTFTADNPGVFFYHCGSDPMIQHIARGMYGVIIVDPKDANALPKADREYVLIQAEHYENPDDKTAMMQNKWSNVVFNGGVFKYDPVHDSEATSWLQAKPGERVRIYFVNAGPNELSSLHPIAGIWDRVYPSGNPKNVQYALQSYLIGAGDAATLDLISPVEGANAIVDHSMRHAHSGAIAVIMFTNDADPEAGRGENILIR 309
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304     


Chain E from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4knse1 E:25-153 automated matches                                                                                               d4knse2 E:154-309 automated matches                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee..................eeeeeee....eeeeee....hhhhhhhh..eeeeeee...........eeeeeeeeee.....hhhhhhh....eeee..................eee.....eeeeeeeee....eeeeee...eeeeee.hhhhhheeee..eee...eeeeeee.....eeeeeee.hhhhhhh..eeeeee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kns E  25 KTVQVTLHAVETDVAYDNKGSTYRAWTFDGKVPGPVVRVTEGDTVEFTLINDKNSKNSHSMDFHAARLDVVEDFESIKPGETKKYTFTADNPGVFFYHCGSDPMIQHIARGMYGVIIVDPKDANALPKADREYVLIQAEHYENPDDKTAMMQNKWSNVVFNGGVFKYDPVHDSEATSWLQAKPGERVRIYFVNAGPNELSSLHPIAGIWDRVYPSGNPKNVQYALQSYLIGAGDAATLDLISPVEGANAIVDHSMRHAHSGAIAVIMFTNDADPEAGRGENILIR 309
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304     


Chain F from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4knsf1 F:25-153 automated matches                                                                                               d4knsf2 F:154-309 automated matches                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee..................eeeeeee....eeeeee....hhhhhhhh..eeeeeee...........eeeeeeeeee.....hhhhhhh....eeee..................eee.....eeeeeeeee....eeeeee...eeeeee.hhhhhheeee..eee...eeeeeee.....eeeeeee.hhhhhhh..eeeeee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kns F  25 KTVQVTLHAVETDVAYDNKGSTYRAWTFDGKVPGPVVRVTEGDTVEFTLINDKNSKNSHSMDFHAARLDVVEDFESIKPGETKKYTFTADNPGVFFYHCGSDPMIQHIARGMYGVIIVDPKDANALPKADREYVLIQAEHYENPDDKTAMMQNKWSNVVFNGGVFKYDPVHDSEATSWLQAKPGERVRIYFVNAGPNELSSLHPIAGIWDRVYPSGNPKNVQYALQSYLIGAGDAATLDLISPVEGANAIVDHSMRHAHSGAIAVIMFTNDADPEAGRGENILIR 309
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304
   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  (1, 12)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Fold: Cupredoxin-like (545)
(-)
Superfamily: Cupredoxins (543)
(-)
Family: automated matches (57)
(-)
Protein domain: automated matches (57)
(-)
Nitrosomonas europaea [TaxId: 228410] (3)
1ad4knsa1A:25-153
1bd4knsa2A:154-309
1cd4knsb1B:25-153
1dd4knsb2B:154-309
1ed4knsc1C:25-153
1fd4knsc2C:154-309
1gd4knsd1D:25-153
1hd4knsd2D:154-309
1id4knse1E:25-153
1jd4knse2E:154-309
1kd4knsf1F:25-153
1ld4knsf2F:154-309

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        Q82VX5_NITEU | Q82VX5: 4knt 4knu

(-) Related Entries Specified in the PDB File

4knt SAME PROTEIN AT PH 8.5
4knu