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(-) Description

Title :  R2-LIKE LIGAND-BINDING OXIDASE WITH AEROBICALLY RECONSTITUTED MN/FE COFACTOR (SHORT SOAK)
 
Authors :  J. J. Griese, M. Hogbom
Date :  24 Aug 15  (Deposition) - 09 Sep 15  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  R2-Like Ligand-Binding Oxidase, Diiron Cofactor, Ribonucleotide Reductase R2 Subunit Fold, Metalloprotein Oxidoreductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Griese, R. Kositzki, P. Schrapers, R. M. Branca, A. Nordstrom, J. Lehtio, M. Haumann, M. Hogbom
Structural Basis For Oxygen Activation At A Heterodinuclear Manganese/Iron Cofactor.
J. Biol. Chem. V. 290 25254 2015
PubMed-ID: 26324712  |  Reference-DOI: 10.1074/JBC.M115.675223

(-) Compounds

Molecule 1 - RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT
    Chains: A
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-46 EK/LIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GK2771
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS (STRAIN HTA426)
    Organism Taxid: 235909
    Strain: HTA426

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2MN31Ligand/IonMANGANESE (III) ION
3PLM1Ligand/IonPALMITIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2MN32Ligand/IonMANGANESE (III) ION
3PLM2Ligand/IonPALMITIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:69 , GLU A:102 , HIS A:105 , FE A:402 , PLM A:403 , HOH A:502 , HOH A:512binding site for residue MN3 A 401
2AC2SOFTWAREGLU A:102 , GLU A:167 , GLU A:202 , HIS A:205 , MN3 A:401 , PLM A:403 , HOH A:512binding site for residue FE A 402
3AC3SOFTWAREGLY A:64 , PHE A:65 , GLU A:69 , GLU A:102 , PHE A:135 , GLU A:167 , LEU A:170 , THR A:177 , GLU A:202 , LEU A:268 , MN3 A:401 , FE A:402 , HOH A:502 , HOH A:512binding site for residue PLM A 403
4AC4SOFTWAREHIS A:130 , HOH A:548binding site for residue FE A 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DCR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DCR)

(-) 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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.....hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dcr A   2 VHHDGFQTVKATIDWEHPMFKLYEKAKRNGKWNPADIDFSQDQKDFASLTSEEKISALPLVAGFSAGEEAVTLDILPMAHALARQGRLEDVLFLTTFMHDEAKHVEMFSRWQQAVGIGQMDLSVFHNDHYKRIFYEALPEAMNRLYADDSPEAVIRAATVYNMIVEGTLAESGYYTFRQIYKKAGLFPGLLQGIDYLNMDEGRHIQFGIYTIQRIVNEDERYYELFIRYMDELWPHVIGYVDYLTELGKRQQQLARTYALEIDYDLLRHYVIKQFNLRKKQISRT 286
                                    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
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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 5DCR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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)

UniProtKB/TrEMBL
        Q5KW80_GEOKA | Q5KW80: 4hr0 4hr4 4hr5 4xb9 4xbv 4xbw 5dco 5dcs 5ekb

(-) Related Entries Specified in the PDB File

4hr0 4HR0 CONTAINS THE SAME PROTEIN WITH AEROBICALLY RECONSTITUTED MN/FE COFACTOR (SHORT SOAK, PROTEIN PURIFIED IN PARTIALLY METAL-BOUND FORM).
4hr4 4HR4 CONTAINS THE SAME PROTEIN WITH ANAEROBICALLY RECONSTITUTED MN/ FE COFACTOR.
4hr5 4HR5 CONTAINS THE SAME PROTEIN WITHOUT METAL COFACTOR.
4xb9 4XB9 CONTAINS THE SAME PROTEIN WITH AEROBICALLY RECONSTITUTED DIIRON COFACTOR (LONG SOAK).
4xbv 4XBV CONTAINS THE SAME PROTEIN WITH ANAEROBICALLY RECONSTITUTED DIIRON COFACTOR.
4xbw 4XBW CONTAINS THE SAME PROTEIN WITH AEROBICALLY RECONSTITUTED DIMANGANESE COFACTOR.
5dco 5DCO CONTAINS THE SAME PROTEIN WITH AEROBICALLY RECONSTITUTED DIIRON COFACTOR (SHORT SOAK).