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(-) Description

Title :  FERREDOXIN FROM PYROCOCCUS FURIOSUS, D14C VARIANT
 
Authors :  M. N. Johannessen, H. E. M. Christensen, P. Harris
Date :  07 Sep 07  (Deposition) - 18 Sep 07  (Release) - 23 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ferredoxin Iron-Sulfur Cluster, Pyrococcus Furiosus, Two Molecules In Asymmetric Unit, Electron Transport, Metal-Binding, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. N. Johannessen, M. S. Nielsen, B. L. Ooi, H. E. M. Christensen, P. Harris
The Crystal Structure Of The All Cysteinyl Coordinated D14C Variant Of [4Fe-4S] Pyrococcus Furiosus Ferredoxin
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FERREDOXIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: FDXA
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS DSM 3638
    Organism Taxid: 186497
    Strain: DSM3638

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1NCO4Ligand/IonCOBALT HEXAMMINE(III)
2SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1NCO2Ligand/IonCOBALT HEXAMMINE(III)
2SF41Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1NCO2Ligand/IonCOBALT HEXAMMINE(III)
2SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:6 , CYS A:11 , ILE A:12 , CYS A:14 , ALA A:15 , CYS A:17 , ALA A:33 , CYS A:56 , VAL A:58 , ILE A:61BINDING SITE FOR RESIDUE SF4 A 101
2AC2SOFTWARELYS A:36 , GLU A:38 , MET A:53 , GLU A:54 , CYS A:56 , PRO A:57 , SER A:59 , HOH A:259BINDING SITE FOR RESIDUE NCO A 102
3AC3SOFTWAREILE A:12 , GLY A:13 , MET A:27 , ASN A:28 , ASP A:29 , GLU A:41 , HOH A:236 , HOH A:254 , HOH A:293BINDING SITE FOR RESIDUE NCO A 103
4AC4SOFTWARECYS B:11 , ILE B:12 , CYS B:14 , ALA B:15 , CYS B:17 , ALA B:33 , CYS B:56 , VAL B:58BINDING SITE FOR RESIDUE SF4 B 101
5AC5SOFTWARELEU B:20 , ASP B:42 , GLU B:43 , GLU B:44 , GLU B:51 , HOH B:223BINDING SITE FOR RESIDUE NCO B 102
6AC6SOFTWARESER A:19 , GLU B:54 , CYS B:56 , HOH B:207BINDING SITE FOR RESIDUE NCO B 103

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:21 -A:48
2B:21 -B:48

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z8Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z8Q)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
14FE4S_FER_2PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.FER_PYRFU3-31
 
36-67
 		  4A:2-30
B:2-30
A:35-66
B:35-66
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
14FE4S_FER_2PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.FER_PYRFU3-31
 
36-67
 		  2A:2-30
-
A:35-66
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
14FE4S_FER_2PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.FER_PYRFU3-31
 
36-67
 		  2-
B:2-30
-
B:35-66

(-) Exons   (0, 0)

(no "Exon" information available for 2Z8Q)

(-) 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:66
 aligned with FER_PYRFU | P29603 from UniProtKB/Swiss-Prot  Length:67

    Alignment length:66
                                    11        21        31        41        51        61      
             FER_PYRFU    2 AWKVSVDQDTCIGDAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 67
               SCOP domains d2z8qa_ A: automated matches                                       SCOP domains
               CATH domains 2z8qA00 A:1-66  [code=3.30.70.20, no name defined]                 CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee........hhhhhhh...eee.....eee......hhhhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -4FE4S_FER_2  PDB: A:2-30     ----4FE4S_FER_2  PDB: A:35-66        PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  2z8q A  1 AWKVSVDQDTCIGCAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 66
                                    10        20        30        40        50        60      


Chain B from PDB  Type:PROTEIN  Length:66
 aligned with FER_PYRFU | P29603 from UniProtKB/Swiss-Prot  Length:67

    Alignment length:66
                                    11        21        31        41        51        61      
             FER_PYRFU    2 AWKVSVDQDTCIGDAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 67
               SCOP domains d2z8qb_ B: automated matches                                       SCOP domains
               CATH domains 2z8qB00 B:1-66  [code=3.30.70.20, no name defined]                 CATH domains
           Pfam domains (1) -----Fer4_13-2z8qB01 B:6-63                                    --- Pfam domains (1)
           Pfam domains (2) -----Fer4_13-2z8qB02 B:6-63                                    --- Pfam domains (2)
         Sec.struct. author .eeeee........hhhhhhh...eee.....eee...ee.hhhhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -4FE4S_FER_2  PDB: B:2-30     ----4FE4S_FER_2  PDB: B:35-66        PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  2z8q B  1 AWKVSVDQDTCIGCAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 66
                                    10        20        30        40        50        60
   Legend:   → Mismatch (orange background)
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  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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: 4Fe-4S (51)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FER_PYRFU | P29603)
molecular function
    GO:0051538    3 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    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:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        FER_PYRFU | P29603: 1siz 1sj1 3pni 4dhv

(-) Related Entries Specified in the PDB File

1siz NATIVE PROTEIN
1sj1 NATIVE PROTEIN