1I8P - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE DETERMINATION OF THE FERROCYTOCHROME C2 FROM RHODOPSEUDOMONAS PALUSTRIS

Authors :   G. Garau, S. Geremia

Date :   15 Mar 01 (Deposition) - 04 Apr 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Electron Carrier, Heme Protein, Cytochrome, C2, Reduced, Rhodopseudomonas Palustris, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Geremia, G. Garau, L. Vaccari, R. Sgarra, M. S. Viezzoli, M. Calligaris, L. Randaccio
Cleavage Of The Iron-Methionine Bond In C-Type Cytochromes: Crystal Structure Of Oxidized And Reduced Cytochrome C(2) From Rhodopseudomonas Palustris And Its Ammonia Complex.
Protein Sci. V. 11 6 2002
PubMed-ID: 11742117 | Reference-DOI: 10.1110/PS.PS.13102
(for further references see the PDB file header)

Molecule 1 - CYTOCHROME C2
	Chains	:	A, B, C, D
	Organism Scientific	:	RHODOPSEUDOMONAS PALUSTRIS
	Organism Taxid	:	1076
	Strain	:	42 OL

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	HEC	4	Ligand/Ion	HEME C
2	PCA	4	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	HEC	1	Ligand/Ion	HEME C
2	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	HEC	1	Ligand/Ion	HEME C
2	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	HEC	1	Ligand/Ion	HEME C
2	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	HEC	1	Ligand/Ion	HEME C
2	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:12 , CYS A:13 , CYS A:16 , HIS A:17 , VAL A:24 , PRO A:26 , ARG A:34 , ALA A:36 , GLY A:37 , PHE A:42 , TYR A:44 , SER A:45 , ASN A:48 , TRP A:58 , TYR A:66 , THR A:91 , LYS A:92 , MET A:93 , PHE A:95 , LEU A:110 , HOH A:117	BINDING SITE FOR RESIDUE HEC A 115
2	AC2	SOFTWARE	THR A:59 , CYS B:13 , CYS B:16 , HIS B:17 , VAL B:24 , GLY B:25 , PRO B:26 , ARG B:34 , ALA B:36 , GLY B:37 , PHE B:42 , TYR B:44 , SER B:45 , ASN B:48 , TRP B:58 , TYR B:66 , THR B:91 , LYS B:92 , MET B:93 , THR B:94 , PHE B:95 , HOH B:126	BINDING SITE FOR RESIDUE HEC B 115
3	AC3	SOFTWARE	GLN C:12 , CYS C:13 , CYS C:16 , HIS C:17 , VAL C:24 , PRO C:26 , ARG C:34 , ALA C:36 , GLY C:37 , PHE C:42 , TYR C:44 , SER C:45 , ASN C:48 , TRP C:58 , TYR C:66 , THR C:91 , LYS C:92 , MET C:93 , PHE C:95 , HOH C:2002	BINDING SITE FOR RESIDUE HEC C 115
4	AC4	SOFTWARE	CYS D:13 , CYS D:16 , HIS D:17 , VAL D:24 , GLY D:25 , PRO D:26 , ARG D:34 , GLY D:37 , PHE D:42 , TYR D:44 , SER D:45 , ASN D:48 , TRP D:58 , TYR D:66 , THR D:91 , LYS D:92 , MET D:93 , THR D:94 , PHE D:95 , HOH D:125	BINDING SITE FOR RESIDUE HEC D 115

(no "SS Bond" information available for 1I8P)

(no "Cis Peptide Bond" information available for 1I8P)

(no "SAP(SNP)/Variant" information available for 1I8P)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC22_RHOPA	26-139	4	A:2-114 B:2-114 C:2-114 D:2-114

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC22_RHOPA	26-139	1	A:2-114 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC22_RHOPA	26-139	1	- B:2-114 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC22_RHOPA	26-139	1	- - C:2-114 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC22_RHOPA	26-139	1	- - - D:2-114

(no "Exon" information available for 1I8P)

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:114
 aligned with CYC22_RHOPA | P00091 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:114
                                    35        45        55        65        75        85        95       105       115       125       135    
          CYC22_RHOPA    26 QDAKAGEAVFKQCMTCHRADKNMVGPALGGVVGRKAGTAAGFTYSPLNHNSGEAGLVWTADNIINYLNDPNAFLKKFLTDKGKADQAVGVTKMTFKLANEQQRKDVVAYLATLK 139
               SCOP domains d1i8pa_ A: Cytochrome c2                                                                                           SCOP domains
               CATH domains -1i8pA00 A:2-114 Cytochrome c                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..............................hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.hhhhhh..........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE CYTC  PDB: A:2-114 UniProt: 26-139                                                                                 PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1i8p A   1 xDAKAGEAVFKQCMTCHRADKNMVGPALAGVVGRKAGTAAGFTYSPLNHNSGEAGLVWTADNIVPYLADPNAFLKKFLTEKGKADQAVGVTKMTFKLANEQQRKDVVAYLATLK 114
                            |       10        20        30        40        50        60        70        80        90       100       110    
                            |                                                                                                                 
                            1-PCA

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with CYC22_RHOPA | P00091 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:114
                                    35        45        55        65        75        85        95       105       115       125       135    
          CYC22_RHOPA    26 QDAKAGEAVFKQCMTCHRADKNMVGPALGGVVGRKAGTAAGFTYSPLNHNSGEAGLVWTADNIINYLNDPNAFLKKFLTDKGKADQAVGVTKMTFKLANEQQRKDVVAYLATLK 139
               SCOP domains d1i8pb_ B: Cytochrome c2                                                                                           SCOP domains
               CATH domains -1i8pB00 B:2-114 Cytochrome c                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..............................hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhh...........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE CYTC  PDB: B:2-114 UniProt: 26-139                                                                                 PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1i8p B   1 xDAKAGEAVFKQCMTCHRADKNMVGPALAGVVGRKAGTAAGFTYSPLNHNSGEAGLVWTADNIVPYLADPNAFLKKFLTEKGKADQAVGVTKMTFKLANEQQRKDVVAYLATLK 114
                            |       10        20        30        40        50        60        70        80        90       100       110    
                            1-PCA

Chain C from PDB  Type:PROTEIN  Length:114
 aligned with CYC22_RHOPA | P00091 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:114
                                    35        45        55        65        75        85        95       105       115       125       135    
          CYC22_RHOPA    26 QDAKAGEAVFKQCMTCHRADKNMVGPALGGVVGRKAGTAAGFTYSPLNHNSGEAGLVWTADNIINYLNDPNAFLKKFLTDKGKADQAVGVTKMTFKLANEQQRKDVVAYLATLK 139
               SCOP domains d1i8pc_ C: Cytochrome c2                                                                                           SCOP domains
               CATH domains -1i8pC00 C:2-114 Cytochrome c                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..............................hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE CYTC  PDB: C:2-114 UniProt: 26-139                                                                                 PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1i8p C   1 xDAKAGEAVFKQCMTCHRADKNMVGPALAGVVGRKAGTAAGFTYSPLNHNSGEAGLVWTADNIVPYLADPNAFLKKFLTEKGKADQAVGVTKMTFKLANEQQRKDVVAYLATLK 114
                            |       10        20        30        40        50        60        70        80        90       100       110    
                            1-PCA

Chain D from PDB  Type:PROTEIN  Length:114
 aligned with CYC22_RHOPA | P00091 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:114
                                    35        45        55        65        75        85        95       105       115       125       135    
          CYC22_RHOPA    26 QDAKAGEAVFKQCMTCHRADKNMVGPALGGVVGRKAGTAAGFTYSPLNHNSGEAGLVWTADNIINYLNDPNAFLKKFLTDKGKADQAVGVTKMTFKLANEQQRKDVVAYLATLK 139
               SCOP domains d1i8pd_ D: Cytochrome c2                                                                                           SCOP domains
               CATH domains -1i8pD00 D:2-114 Cytochrome c                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..............................hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhh...........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE CYTC  PDB: D:2-114 UniProt: 26-139                                                                                 PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1i8p D   1 xDAKAGEAVFKQCMTCHRADKNMVGPALAGVVGRKAGTAAGFTYSPLNHNSGEAGLVWTADNIVPYLADPNAFLKKFLTEKGKADQAVGVTKMTFKLANEQQRKDVVAYLATLK 114
                            |       10        20        30        40        50        60        70        80        90       100       110    
                            1-PCA

Legend:		→ Mismatch	(orange background)
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		→ 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(

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Superfamilies( (-)

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)

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)

Class: All alpha proteins (14657)

Fold: Cytochrome c (308)

Superfamily: Cytochrome c (308)

Family: monodomain cytochrome c (197)

Protein domain: Cytochrome c2 (21)

Rhodopseudomonas palustris [TaxId: 1076] (4)

1a	d1i8pa_	A:
1b	d1i8pb_	B:
1c	d1i8pc_	C:
1d	d1i8pd_	D:

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)

Rhodopseudomonas palustris. Organism_taxid: 1076. Strain: 42 ol (4)

1a	1i8pA00	A:2-114
1b	1i8pB00	B:2-114
1c	1i8pC00	C:2-114
1d	1i8pD00	D:2-114

(no "Pfam Domain" information available for 1I8P)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CYC22_RHOPA | P00091)

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.

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	CYC22_RHOPA \| P00091	:	1fj0 1hh7 1i8o

1fj0	STRUCTURE DETERMINATION OF THE FERRICYTOCHROME C2 FROM RHODOPSEUDOMONAS PALUSTRIS
1i8o	RHODOPSEUDOMONAS PALUSTRIS CYT C2 AMMONIA COMPLEX AT 1.15 ANGSTROM RESOLUTION

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