2CXB - JenaLib

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Title :   CRYSTALLIZATION AND X-RAY STRUCTURE DETERMINATION OF CYTOCHROME C2 FROM RHODOBACTER SPHAEROIDES IN THREE CRYSTAL FORMS

Authors :   H. L. Axelrod, G. Feher, J. P. Allen, A. J. Chirino, M. W. Day, B. T. Hsu, D. C. Rees

Date :   21 Apr 94 (Deposition) - 15 Oct 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Electron Transport (Cytochrome) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. L. Axelrod, G. Feher, J. P. Allen, A. J. Chirino, M. W. Day, B. T. Hsu, D. C. Rees
Crystallization And X-Ray Structure Determination Of Cytochrome C2 From Rhodobacter Sphaeroides In Three Crystal Forms.
Acta Crystallogr. , Sect. D V. 50 596 1994
PubMed-ID: 15299423 | Reference-DOI: 10.1107/S0907444994001319
(for further references see the PDB file header)

Molecule 1 - CYTOCHROME C2
	Chains	:	A, B
	Organism Scientific	:	RHODOBACTER SPHAEROIDES
	Organism Taxid	:	1063

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

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

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:15 , THR A:17 , CYS A:18 , HIS A:19 , THR A:36 , ARG A:46 , ALA A:48 , GLY A:49 , TYR A:57 , GLY A:58 , MET A:61 , TRP A:71 , TYR A:79 , GLY A:98 , LYS A:99 , MET A:100 , PHE A:102 , HOH A:126 , HOH A:127 , HOH A:128 , ALA B:66	BINDING SITE FOR RESIDUE HEM A 125
2	AC2	SOFTWARE	ALA A:66 , CYS B:15 , THR B:17 , CYS B:18 , HIS B:19 , THR B:36 , ARG B:46 , ALA B:48 , GLY B:49 , TYR B:57 , GLY B:58 , MET B:61 , TRP B:71 , TYR B:79 , LYS B:99 , MET B:100 , PHE B:102 , HOH B:141 , HOH B:142 , HOH B:143	BINDING SITE FOR RESIDUE HEM B 125

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC2_RHOSH	3-121	2	A:3-121 B:3-121
1	CYTC	PS51007	Cytochrome c family profile.	CYC2_RHOS4	24-142	2	A:3-121 B:3-121

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC2_RHOSH	3-121	1	A:3-121 -
1	CYTC	PS51007	Cytochrome c family profile.	CYC2_RHOS4	24-142	1	A:3-121 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC2_RHOSH	3-121	1	- B:3-121
1	CYTC	PS51007	Cytochrome c family profile.	CYC2_RHOS4	24-142	1	- B:3-121

(no "Exon" information available for 2CXB)

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:123
 aligned with CYC2_RHOS4 | Q3J164 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:123
                                    32        42        52        62        72        82        92       102       112       122       132       142   
           CYC2_RHOS4    23 EGDPEAGAKAFNQCQTCHVIVDDSGTTIAGRNAKTGPNLYGVVGRTAGTQADFKGYGEGMKEAGAKGLAWDEEHFVQYVQDPTKFLKEYTGDAKAKGKMTFKLKKEADAHNIWAYLQQVAVRP 145
               SCOP domains d2cxba_ A: Cytochrome c2                                                                                                    SCOP domains
               CATH domains 2cxbA00 A:2-124 Cytochrome c                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..ee.....eee............................hhhhhhhh.....hhhhhhhhhh.hhhhhhhhh...............hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -CYTC  PDB: A:3-121 UniProt: 24-142                                                                                     --- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cxb A   2 EGDPEAGAKAFNQCQTCHVIVDDSGTTIAGRNAKTGPNLYGVVGRTAGTQADFKGYGEGMKEAGAKGLAWDEEHFVQYVQDPTKFLKEYTGDAKAKGKMTFKLKKEADAHNIWAYLQQVAVRP 124
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain A from PDB  Type:PROTEIN  Length:123
 aligned with CYC2_RHOSH | P0C0X8 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:123
                                    11        21        31        41        51        61        71        81        91       101       111       121   
           CYC2_RHOSH     2 EGDPEAGAKAFNQCQTCHVIVDDSGTTIAGRNAKTGPNLYGVVGRTAGTQADFKGYGEGMKEAGAKGLAWDEEHFVQYVQDPTKFLKEYTGDAKAKGKMTFKLKKEADAHNIWAYLQQVAVRP 124
               SCOP domains d2cxba_ A: Cytochrome c2                                                                                                    SCOP domains
               CATH domains 2cxbA00 A:2-124 Cytochrome c                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..ee.....eee............................hhhhhhhh.....hhhhhhhhhh.hhhhhhhhh...............hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: A:3-121 UniProt: 3-121                                                                                      --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cxb A   2 EGDPEAGAKAFNQCQTCHVIVDDSGTTIAGRNAKTGPNLYGVVGRTAGTQADFKGYGEGMKEAGAKGLAWDEEHFVQYVQDPTKFLKEYTGDAKAKGKMTFKLKKEADAHNIWAYLQQVAVRP 124
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with CYC2_RHOS4 | Q3J164 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:123
                                    32        42        52        62        72        82        92       102       112       122       132       142   
           CYC2_RHOS4    23 EGDPEAGAKAFNQCQTCHVIVDDSGTTIAGRNAKTGPNLYGVVGRTAGTQADFKGYGEGMKEAGAKGLAWDEEHFVQYVQDPTKFLKEYTGDAKAKGKMTFKLKKEADAHNIWAYLQQVAVRP 145
               SCOP domains d2cxbb_ B: Cytochrome c2                                                                                                    SCOP domains
               CATH domains 2cxbB00 B:2-124 Cytochrome c                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..ee.....eee............................hhhhhhhh.....hhhhhhhhhh.hhhhhhhhh...............hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -CYTC  PDB: B:3-121 UniProt: 24-142                                                                                     --- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cxb B   2 EGDPEAGAKAFNQCQTCHVIVDDSGTTIAGRNAKTGPNLYGVVGRTAGTQADFKGYGEGMKEAGAKGLAWDEEHFVQYVQDPTKFLKEYTGDAKAKGKMTFKLKKEADAHNIWAYLQQVAVRP 124
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with CYC2_RHOSH | P0C0X8 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:123
                                    11        21        31        41        51        61        71        81        91       101       111       121   
           CYC2_RHOSH     2 EGDPEAGAKAFNQCQTCHVIVDDSGTTIAGRNAKTGPNLYGVVGRTAGTQADFKGYGEGMKEAGAKGLAWDEEHFVQYVQDPTKFLKEYTGDAKAKGKMTFKLKKEADAHNIWAYLQQVAVRP 124
               SCOP domains d2cxbb_ B: Cytochrome c2                                                                                                    SCOP domains
               CATH domains 2cxbB00 B:2-124 Cytochrome c                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..ee.....eee............................hhhhhhhh.....hhhhhhhhhh.hhhhhhhhh...............hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: B:3-121 UniProt: 3-121                                                                                      --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cxb B   2 EGDPEAGAKAFNQCQTCHVIVDDSGTTIAGRNAKTGPNLYGVVGRTAGTQADFKGYGEGMKEAGAKGLAWDEEHFVQYVQDPTKFLKEYTGDAKAKGKMTFKLKKEADAHNIWAYLQQVAVRP 124
                                    11        21        31        41        51        61        71        81        91       101       111       121

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 Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Cytochrome c (308)

Superfamily: Cytochrome c (308)

Family: monodomain cytochrome c (197)

Protein domain: Cytochrome c2 (21)

Rhodobacter sphaeroides [TaxId: 1063] (5)

1a	d2cxba_	A:
1b	d2cxbb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome Bc1 Complex; Chain D, domain 2 (279)

Homologous Superfamily: Cytochrome c (279)

Rhodobacter sphaeroides. Organism_taxid: 1063 (7)

1a	2cxbA00	A:2-124
1b	2cxbB00	B:2-124

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (CYC2_RHOSH | P0C0X8)

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: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.
	GO:0015979	photosynthesis	The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
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).

Chain A,B (CYC2_RHOS4 | Q3J164)

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: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.
	GO:0015979	photosynthesis	The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
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 Unit
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	CYC2_RHOS4 \| Q3J164	:	1cxa 1cxc 1l9b 1l9j
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