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Title :   THE CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RUBRIVIVAX GELATINOSUS AT 1.3 A RESOLUTION AND PH 8.0

Authors :   S. Benini, S. Ciurli, W. R. Rypniewski, K. S. Wilson

Date :   30 Oct 06 (Deposition) - 06 Nov 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.29

Chains :   Asym./Biol. Unit : A,B

Keywords :   C', Heme, Iron, Transport, Cytochrome, Metal-Binding, Electron Transfer, Electron Transport, Rubrivivax Gelatinosus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Benini, W. R. Rypniewski, K. S. Wilson, S. Ciurli
High Resolution Crystal Structure Of Rubrivivax Gelatinosus Cytochrome C'.
J. Inorg. Biochem. V. 102 1322 2008
PubMed-ID: 18295896 | Reference-DOI: 10.1016/J.JINORGBIO.2008.01.017

Molecule 1 - CYTOCHROME C'
	Chains	:	A, B
	Organism Scientific	:	RUBRIVIVAX GELATINOSUS
	Organism Taxid	:	28068
	Other Details	:	DSMZ
	Strain	:	DSM 1709

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:12 , GLN A:13 , PHE A:16 , THR A:17 , ILE A:19 , PHE A:59 , THR A:69 , GLU A:70 , PHE A:82 , ALA A:86 , PHE A:89 , CYS A:119 , CYS A:122 , HIS A:123 , LYS A:127 , HOH A:2174 , HOH A:2255 , HOH A:2256 , HOH A:2257 , HOH A:2258 , HOH A:2259 , HOH A:2260	BINDING SITE FOR RESIDUE HEM A1129
2	AC2	SOFTWARE	ARG B:12 , GLN B:13 , PHE B:16 , THR B:17 , ILE B:19 , THR B:69 , GLU B:70 , PHE B:82 , ALA B:85 , ALA B:86 , PHE B:89 , CYS B:119 , CYS B:122 , HIS B:123 , LYS B:127 , HOH B:2189 , HOH B:2190 , HOH B:2283 , HOH B:2284 , HOH B:2285	BINDING SITE FOR RESIDUE HEM B1129

(no "SS Bond" information available for 2J8W)

(no "Cis Peptide Bond" information available for 2J8W)

(no "SAP(SNP)/Variant" information available for 2J8W)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTCII	PS51009	Cytochrome c class II profile.	CYCP_RUBGE	7-128	2	A:7-128 B:7-128

(no "Exon" information available for 2J8W)

Asymmetric/Biological 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:129
 aligned with CYCP_RUBGE | P00142 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
           CYCP_RUBGE     1 QFQKPGDAIEYRQSAFTLIANHFGRVAAMAQGKAPFDAKVAAENIALVSTLSKLPLTAFGPGTDKGHGTEAKPAVWSDAAGFKAAADKFAAAVDKLDAAGKTGDFAQIKAAVGETGGACKGCHDKFKEK 129
               SCOP domains d2j8wa_ A: automated matches                                                                                                      SCOP domains
               CATH domains 2j8wA00 A:1-129  [code=1.20.120.10, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------CYTCII  PDB: A:7-128 UniProt: 7-128                                                                                       - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j8w A   1 QFQKPGDAIEYRQSAFTLIANHFGRVAAMAQGKAPFDAKVAAENIALVSTLSKLPLTAFGPGTDKGHGTEAKPAVWSDAAGFKAAADKFAAAVDKLDAAGKTGDFAQIKAAVGETGGACKGCHDKFKEK 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with CYCP_RUBGE | P00142 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
           CYCP_RUBGE     1 QFQKPGDAIEYRQSAFTLIANHFGRVAAMAQGKAPFDAKVAAENIALVSTLSKLPLTAFGPGTDKGHGTEAKPAVWSDAAGFKAAADKFAAAVDKLDAAGKTGDFAQIKAAVGETGGACKGCHDKFKEK 129
               SCOP domains d2j8wb_ B: automated matches                                                                                                      SCOP domains
               CATH domains 2j8wB00 B:1-129  [code=1.20.120.10, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------CYTCII  PDB: B:7-128 UniProt: 7-128                                                                                       - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j8w B   1 QFQKPGDAIEYRQSAFTLIANHFGRVAAMAQGKAPFDAKVAAENIALVSTLSKLPLTAFGPGTDKGHGTEAKPAVWSDAAGFKAAADKFAAAVDKLDAAGKTGDFAQIKAAVGETGGACKGCHDKFKEK 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Four-helical up-and-down bundle (308)

Superfamily: Cytochromes (82)

Family: Cytochrome c'-like (44)

Protein domain: automated matches (27)

Rubrivivax gelatinosus [TaxId: 28068] (1)

1a	d2j8wa_	A:
1b	d2j8wb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Four Helix Bundle (Hemerythrin (Met), subunit A) (300)

Homologous Superfamily: [code=1.20.120.10, no name defined] (45)

Rubrivivax gelatinosus. Organism_taxid: 28068. Strain: dsm 1709. (1)

1a	2j8wA00	A:1-129
1b	2j8wB00	B:1-129

(no "Pfam Domain" information available for 2J8W)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CYCP_RUBGE | P00142)

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).

Asymmetric/Biological Unit
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	CYCP_RUBGE \| P00142	:	1jaf 2j9b

1jaf	CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RHODOCYCLUS GELATINOSUS AT 2.5 ANGSTOMS RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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