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(-) Description

Title :  SPECTROSCOPICALLY-VALIDATED STRUCTURE OF FERRIC CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS
 
Authors :  D. Kekilli, F. Dworkowski, S. Antonyuk, M. A. Hough
Date :  30 Oct 13  (Deposition) - 21 May 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Electron Transport, Resonance Raman, Validation, Gas Sensor, Ligand Discrimination, Haem, Heme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kekilli, F. S. Dworkowski, G. Pompidor, M. R. Fuchs, C. R. Andrew, S. Antonyuk, R. W. Strange, R. R. Eady, S. S. Hasnain, M. A. Hough
Fingerprinting Redox And Ligand States In Haemprotein Crystal Structures Using Resonance Raman Spectroscopy.
Acta Crystallogr. , Sect. D V. 70 1289 2014
PubMed-ID: 24816098  |  Reference-DOI: 10.1107/S1399004714004039

(-) Compounds

Molecule 1 - CYTOCHROME C'
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: ACHROMOBACTER XYLOSOXIDANS
    Organism Taxid: 85698
    Synonym: CYTOCHROME C PRIME

 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
1HEC1Ligand/IonHEME C
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1HEC2Ligand/IonHEME C
2PCA2Mod. Amino AcidPYROGLUTAMIC ACID
3SO44Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:12 , GLN A:13 , LEU A:16 , THR A:17 , TRP A:56 , GLY A:65 , ASP A:67 , ALA A:68 , GLN A:83 , PHE A:86 , CYS A:116 , CYS A:119 , HIS A:120 , TYR A:123 , ARG A:124 , SO4 A:1128 , HOH A:2059 , HOH A:2254 , HOH A:2255 , HOH A:2256BINDING SITE FOR RESIDUE HEC A 129
2AC2SOFTWAREARG A:124 , HEC A:129 , HOH A:2257 , HOH A:2258 , HOH A:2259BINDING SITE FOR RESIDUE SO4 A1128
3AC3SOFTWARESER A:74 , ASP A:75 , ALA A:76 , ALA A:77 , LYS A:104 , HOH A:2261BINDING SITE FOR RESIDUE SO4 A1129

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CDA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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)

(no "Exon" information available for 4CDA)

(-) 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:127
 aligned with CYCP_ALCXX | P00138 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:127
                                    10        20        30        40        50        60        70        80        90       100       110       120       
           CYCP_ALCXX     1 QFAKPEDAVKYRQSALTLMASHFGRMTPVVKGQAPYDAAQIKANVEVLKTLSALPWAAFGPGTEGGDARPEIWSDAASFKQKQQAFQDNIVKLSAAADAGDLDKLRAAFGDVGASCKACHDAYRKKK 127
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- 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
                 4cda A   1 xFAKPEDAVKYRQSALTLMASHFGRMTPVVKGQAPYDAAQIKANVEVLKTLSALPWAAFGPGTEGGDARPEIWSDAASFKQKQQAFQDNIVKLSAAADAGDLDKLRAAFGDVGASCKACHDAYRKKK 127
                            |       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  (0, 0)

(no "SCOP Domain" information available for 4CDA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  4cda
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 Related Entries

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

UniProtKB/Swiss-Prot
        CYCP_ALCXX | P00138: 1cgn 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 3ztz 3zwi 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

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