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(-) Description

Title :  CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND L16G VARIANT AT 1.05 A RESOLUTION: UNRESTRAINT REFINEMENT
 
Authors :  S. V. Antonyuk, N. Rustage, R. R. Eady, S. S. Hasnain
Date :  12 Jul 11  (Deposition) - 05 Oct 11  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Electron Transport, Haemoprotein, 4-Helix Bundle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. V. Antonyuk, N. Rustage, C. A. Petersen, J. L. Arnst, D. J. Heyes, R. Sharma, N. G. Berry, N. S. Scrutton, R. R. Eady, C. R. Andrew, S. S. Hasnain
Carbon Monoxide Poisoning Is Prevented By The Energy Costs Of Conformational Changes In Gas- Binding Haemproteins.
Proc. Natl. Acad. Sci. Usa V. 108 15780 2011
PubMed-ID: 21900609  |  Reference-DOI: 10.1073/PNAS.1109051108

(-) Compounds

Molecule 1 - CYTOCHROME C'
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPEC86
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificACHROMOBACTER XYLOSOXIDANS
    Organism Taxid85698

 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, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CMO1Ligand/IonCARBON MONOXIDE
2HEC1Ligand/IonHEME C
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1CMO2Ligand/IonCARBON MONOXIDE
2HEC2Ligand/IonHEME C
3PCA2Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:12 , GLN A:13 , GLY A:16 , MET A:19 , ALA A:20 , TRP A:56 , GLY A:65 , ASP A:67 , ALA A:68 , ILE A:72 , PHE A:79 , LYS A:82 , GLN A:83 , PHE A:86 , CYS A:116 , CYS A:119 , HIS A:120 , TYR A:123 , ARG A:124 , CMO A:1127 , HOH A:2066 , HOH A:2272 , HOH A:2273 , HOH A:2274BINDING SITE FOR RESIDUE HEC A1126
2AC2SOFTWAREGLY A:16 , MET A:19 , PRO A:55 , HEC A:1126BINDING SITE FOR RESIDUE CMO A1127

(-) SS Bonds  (0, 0)

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

(-) 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
1CYTCIIPS51009 Cytochrome c class II profile.CYCP_ALCXX7-125  1A:7-125
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCIIPS51009 Cytochrome c class II profile.CYCP_ALCXX7-125  2A:7-125

(-) Exons   (0, 0)

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(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:125
 aligned with CYCP_ALCXX | P00138 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
           CYCP_ALCXX     1 QFAKPEDAVKYRQSALTLMASHFGRMTPVVKGQAPYDAAQIKANVEVLKTLSALPWAAFGPGTEGGDARPEIWSDAASFKQKQQAFQDNIVKLSAAADAGDLDKLRAAFGDVGASCKACHDAYRK 125
               SCOP domains d3ztza_ A: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------CYTCII  PDB: A:7-125 UniProt: 7-125                                                                                     PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ztz A   1 xFAKPEDAVKYRQSAGTLMASHFGRMTPVVKGQAPYDAAQIKANVEVLKTLSALPWAAFGPGTEGGDARPEIWSDAASFKQKQQAFQDNIVKLSAAADAGDLDKLRAAFGDVGASCKACHDAYRK 125
                            |       10        20        30        40        50        60        70        80        90       100       110       120     
                            |                                                                                                                            
                            1-PCA                                                                                                                        

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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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (CYCP_ALCXX | P00138)
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:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    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:0022900    electron transport chain    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: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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        CYCP_ALCXX | P001381cgn 1cgo 1e83 1e84 1e85 1e86 2xl6 2xl8 2xld 2xle 2xlh 2xlm 2xlo 2xlv 2xlw 2xm0 2xm4 2ykz 2yl0 2yl1 2yl3 2yl7 2yld 2ylg 2yli 3zqv 3zqy 3ztm 3zwi 4cda 4cdv 4cdy 4cip 4cjg 4cjo 4d4n 4d4x 4wgy 4wgz 5agf 5jli 5jp7 5jra 5js5 5jsl 5jt4 5jua 5jve

(-) Related Entries Specified in the PDB File

1cgn CYTOCHROME C'
1cgo CYTOCHROME C'
1e83 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - OXIDIZED STRUCTURE
1e84 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE
1e85 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE WITH NO BOUND TO PROXIMAL SIDE OF HEME
1e86 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE WITH CO BOUND TO DISTAL SIDE OF HEME
2xl6 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124A VARIANT WITH BOUND NO
2xl8 REDUCED STRUCTURE OF R124F MUTANT OF CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS
2xld CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124Q VARIANT
2xle CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124K VARIANT WITH BOUND NO
2xlh REDUCED STRUCTURE OF R124A MUTANT OF CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS
2xlm CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS RECOMBINANT NATIVE WITH BOUND NO
2xlo CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124E VARIANT WITH BOUND NO
2xlv CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124F VARIANT WITH BOUND NO
2xlw CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124Q VARIANT WITH BOUND NO
2xm0 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124K VARIANT
2xm4 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124E VARIANT
2ykz RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS AT 0.84 A RESOLUTION: RESTRAINED REFINEMENT
2yl0 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: AS ISOLATED L16A VARIANT AT 0.95 A RESOLUTION
2yl1 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND L16A VARIANT AT 1.03 A RESOLUTION - RESTRAINT REFINEMENT
2yl3 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND L16G VARIANT AT 1.04 A RESOLUTION
2yl7 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: AS ISOLATED L16G VARIANT AT 0.9 A RESOLUTION - RESTRAINT REFINEMENT
2yld RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND AT 1.25 A
2ylg CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: ASCORBATE AND CARBON MONOOXIDE BOUND L16A VARIANT AT 1 .05 A RESOLUTION
2yli RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS IN ITS FERROUS FORM AT 1.45 A
3zqv RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS AT 0.84 A RESOLUTION: NON-RESTRAINED REFINEMENT
3zqy CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND L16A VARIANT AT 1.03 A RESOLUTION- NON-RESTRAINT REFINEMENT
3ztm CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: AS ISOLATED L16G VARIANT AT 1.04 A RESOLUTION : UNRESTRAINT REFINEMENT
3zwi RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND AT 1.25 A: UNRESTRAINT REFINEMENT