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(-) Description

Title :  NEUTRON STRUCTURE OF PERDEUTERATED RUBREDOXIN USING 48 HOURS 3RD PASS DATA
 
Authors :  P. Munshi, C. -L. Chung, M. P. Blakeley, K. L. Weiss, D. A. A. Myles, F. Mei
Date :  07 Jul 11  (Deposition) - 28 Dec 11  (Release) - 04 Jan 12  (Revision)
Method :  NEUTRON DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Keywords :  Iron, Metal-Binding, Transport, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Munshi, S. L. Chung, M. P. Blakeley, K. L. Weiss, D. A. Myles, F. Meilleur
Rapid Visualization Of Hydrogen Positions In Protein Neutro Crystallographic Structures.
Acta Crystallogr. , Sect. D V. 68 35 2012
PubMed-ID: 22194331  |  Reference-DOI: 10.1107/S0907444911048402

(-) Compounds

Molecule 1 - RUBREDOXIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PF1282, RUB
    Organism Scientific: PYROCOCCUS FURIOSUS DSM 3638
    Organism Taxid: 186497
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / VC1
    Synonym: RD

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 34)

Asymmetric Unit (2, 34)
No.NameCountTypeFull Name
1DOD33Ligand/Ion
2FE1Ligand/IonFE (III) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1DOD-1Ligand/Ion
2FE-1Ligand/IonFE (III) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:5 , CYS A:8 , CYS A:38 , CYS A:41BINDING SITE FOR RESIDUE FE A 54

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SS2)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUBREDOXINPS00202 Rubredoxin signature.RUBR_PYRFU33-43  1A:32-42
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUBREDOXINPS00202 Rubredoxin signature.RUBR_PYRFU33-43  1A:32-42

(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:51
 aligned with RUBR_PYRFU | P24297 from UniProtKB/Swiss-Prot  Length:54

    Alignment length:51
                                    11        21        31        41        51 
            RUBR_PYRFU    2 AKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKL 52
               SCOP domains d3ss2a_ A: Rubredoxin                               SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eee....hhhhh.....hhhhh...........hhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------RUBREDOXIN --------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                  3ss2 A  1 AKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKL 51
                                    10        20        30        40        50
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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  (1, 1)

Asymmetric Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SS2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SS2)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (RUBR_PYRFU | P24297)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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  RUBR_PYRFU | P24297
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 Related Entries

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

UniProtKB/Swiss-Prot
        RUBR_PYRFU | P24297: 1bq8 1bq9 1brf 1caa 1cad 1iu5 1iu6 1qcv 1rwd 1vcx 1zrp 2pvx 3kyu 3kyv 3kyw 3kyx 3kyy 3ryg 3rz6 3rzt 4ar3 4ar4 4ar5 4ar6 4k9f 5ai2 5ai3 5nw3

(-) Related Entries Specified in the PDB File

3kyx X-RAY AND NEUTRON JOINT REFINEMENT
3ryg REFINEMENT USING 128 HOURS NEUTRON DATA ONLY
3rz6 REFINEMENT USING 40 HOURS 1ST PASS NEUTRON DATA ONLY
3rzr REFINEMENT USING 40 HOURS 2ND PASS NEUTRON DATA ONLY
3rzt REFINEMENT USING JUST 14 HOURS NEUTRON DATA ONLY