1E2V - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   N153Q MUTANT OF CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII

Authors :   G. Sainz, C. J. Carrell, M. V. Ponamarev, G. M. Soriano, W. A. Cramer, J. L. Smith

Date :   29 May 00 (Deposition) - 04 Aug 00 (Release) - 05 Sep 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Electron Transport, Internal Water Chain, Photosynthetic Function Impaired (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Sainz, C. J. Carrell, M. V. Ponamarev, G. M. Soriano, W. A. Cramer, J. L. Smith
Interruption Of The Internal Water Chain Of Cytochrome F Impairs Photosynthetic Function
Biochemistry V. 39 9164 2000
PubMed-ID: 10924110 | Reference-DOI: 10.1021/BI0004596

Molecule 1 - CYTOCHROME F
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	CCMABCDEFGH
	Expression System Plasmid	:	PUCPF2
	Expression System Strain	:	MV1190
	Expression System Taxid	:	562
	Gene	:	PETA
	Mutation	:	YES
	Organism Scientific	:	CHLAMYDOMONAS REINHARDTII
	Organism Taxid	:	3055

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	HEC	3	Ligand/Ion	HEME C

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	HEC	1	Ligand/Ion	HEME C

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	HEC	1	Ligand/Ion	HEME C

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	HEC	1	Ligand/Ion	HEME C

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:119 , TYR A:123 , HOH A:2243	BINDING SITE FOR RESIDUE ACT A 901
2	AC2	SOFTWARE	GLN A:220 , THR A:221 , GLN A:226 , HOH A:2413 , PRO B:461 , ASP B:462 , GLY B:463	BINDING SITE FOR RESIDUE ACT A 902
3	AC3	SOFTWARE	ASN B:308 , TYR B:309 , ALA B:310 , HOH B:2379 , HOH B:2380	BINDING SITE FOR RESIDUE ACT B 901
4	AC4	SOFTWARE	TYR A:1 , PHE A:4 , CYS A:21 , CYS A:24 , HIS A:25 , GLN A:59 , ALA A:62 , LEU A:69 , ASN A:70 , VAL A:71 , GLY A:72 , MET A:73 , GLN A:153 , GLY A:155 , ARG A:156 , GLY A:157 , VAL A:159 , TYR A:160 , HOH A:2410 , HOH A:2411 , HOH A:2412 , ASN C:616 , HOH C:2134	BINDING SITE FOR RESIDUE HEC A 900
5	AC5	SOFTWARE	TYR B:301 , PRO B:302 , PHE B:304 , ALA B:305 , CYS B:321 , CYS B:324 , HIS B:325 , GLN B:359 , LEU B:369 , ASN B:370 , VAL B:371 , GLY B:372 , MET B:373 , GLN B:453 , GLY B:455 , ARG B:456 , GLY B:457 , VAL B:459 , TYR B:460 , PRO B:461 , HOH B:2376 , HOH B:2377 , HOH B:2378	BINDING SITE FOR RESIDUE HEC B 900
6	AC6	SOFTWARE	TYR C:601 , PHE C:604 , ALA C:605 , CYS C:621 , CYS C:624 , HIS C:625 , GLN C:659 , LEU C:669 , ASN C:670 , VAL C:671 , GLY C:672 , MET C:673 , GLN C:753 , GLY C:755 , ARG C:756 , GLY C:757 , VAL C:759 , TYR C:760 , PRO C:761 , HOH C:2391 , HOH C:2392 , HOH C:2393	BINDING SITE FOR RESIDUE HEC C 900

(no "SS Bond" information available for 1E2V)

Asymmetric Unit

No.	Residues
1	Gly A:116	-	Pro A:117
2	Gly B:416	-	Pro B:417
3	Gly C:716	-	Pro C:717

(no "SAP(SNP)/Variant" information available for 1E2V)

(no "PROSITE Motif" information available for 1E2V)

(no "Exon" information available for 1E2V)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:251
 aligned with CYF_CHLRE | P23577 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:251
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281 
            CYF_CHLRE    32 YPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTVFEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPGKKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGNRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSIEKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPAR 282
               SCOP domains d1e2va1 A:1-168,A:233-251 Cytochrome f, large domain                                                                                                                    d1e2va2 A:169-232 Cytochrome f, small domain                    d1e2va1             SCOP domains
               CATH domains 1e2vA01 A:1-170,A:231-251  [code=2.60.40.830, no name defined]                                                                                                            1e2vA02 A:171-230  [code=2.40.50.100, no name defined]      1e2vA01               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..........hhhhh.......eee.........eeeeeee....................eeeeee........hhhhhhhhhhhhhh.............eeee....hhhhheeeeeee.............eeeeeeeeee.......................eeeeeee.......eeeeee.....eeeeee...........................eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e2v A   1 YPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTVFEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPGKKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGQRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSIEKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPAR 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain B from PDB  Type:PROTEIN  Length:251
 aligned with CYF_CHLRE | P23577 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:251
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281 
            CYF_CHLRE    32 YPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTVFEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPGKKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGNRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSIEKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPAR 282
               SCOP domains d1e2vb1 B:301-468,B:533-551 Cytochrome f, large domain                                                                                                                  d1e2vb2 B:469-532 Cytochrome f, small domain                    d1e2vb1             SCOP domains
               CATH domains 1e2vB01 B:301-470,B:531-551  [code=2.60.40.830, no name defined]                                                                                                          1e2vB02 B:471-530  [code=2.40.50.100, no name defined]      1e2vB01               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..........hhhhh.......eee...eee...eeeeeee....................eeeeee........hhhhhhhhhhhhhh.............eeee....hhhhheeeeeee.............eeeeeeeeee.......................eeeeeee.......eeeeee.....eeeeee...........................eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e2v B 301 YPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTVFEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPGKKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGQRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSIEKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPAR 551
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550

Chain C from PDB  Type:PROTEIN  Length:251
 aligned with CYF_CHLRE | P23577 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:251
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281 
            CYF_CHLRE    32 YPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTVFEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPGKKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGNRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSIEKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPAR 282
               SCOP domains d1e2vc1 C:601-768,C:833-851 Cytochrome f, large domain                                                                                                                  d1e2vc2 C:769-832 Cytochrome f, small domain                    d1e2vc1             SCOP domains
               CATH domains 1e2vC01 C:601-770,C:831-851  [code=2.60.40.830, no name defined]                                                                                                          1e2vC02 C:771-830  [code=2.40.50.100, no name defined]      1e2vC01               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..........hhhhh.......eee...eee...eeeeeee....................eeeeee........hhhhhhhhhhhhhh.............eeee....hhhhheeeeeee.............eeeeeeeeee.......................eeeeeee.......eeeeee.....eeeeee...........................eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e2v C 601 YPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTVFEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPGKKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGQRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSIEKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPAR 851
                                   610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850

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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Barrel-sandwich hybrid (185)

Superfamily: Rudiment single hybrid motif (69)

Family: Cytochrome f, small domain (12)

Protein domain: Cytochrome f, small domain (12)

Green alga (Chlamydomonas reinhardtii) [TaxId: 3055] (6)

1a	d1e2va2	A:169-232
1b	d1e2vb2	B:469-532
1c	d1e2vc2	C:769-832

Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f (364)

Superfamily: Cytochrome f, large domain (12)

Family: Cytochrome f, large domain (12)

Protein domain: Cytochrome f, large domain (12)

Green alga (Chlamydomonas reinhardtii) [TaxId: 3055] (6)

2a	d1e2va1	A:1-168,A:233-251
2b	d1e2vb1	B:301-468,B:533-551
2c	d1e2vc1	C:601-768,C:833-851

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: [code=2.40.50.100, no name defined] (113)

Chlamydomonas reinhardtii. Organism_taxid: 3055. (4)

1a	1e2vA02	A:171-230
1b	1e2vB02	B:471-530
1c	1e2vC02	C:771-830

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.830, no name defined] (19)

Chlamydomonas reinhardtii. Organism_taxid: 3055. (4)

2a	1e2vA01	A:1-170,A:231-251
2b	1e2vB01	B:301-470,B:531-551
2c	1e2vC01	C:601-770,C:831-851

(no "Pfam Domain" information available for 1E2V)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (CYF_CHLRE | P23577)

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: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:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009535	chloroplast thylakoid membrane	The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0031361	integral component of thylakoid membrane	The component of the thylakoid membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
	GO:0009579	thylakoid	A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

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	Cis Peptide Bonds
		Gly A:116 - Pro A:117	[ RasMol ]
		Gly B:416 - Pro B:417	[ RasMol ]
		Gly C:716 - Pro C:717	[ RasMol ]

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	CYF_CHLRE \| P23577	:	1cfm 1e2w 1e2z 1ewh 1q90

1cfm	WILD TYPE CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII
1ci3	WILD TYPE CYTOCHROME F FROM PHORMIDIUM LAMINOSUM
1e2w	N168F MUTANT OF CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII
1e2z	Q158L MUTANT OF CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII
1ewh	STRUCTURE OF CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII
1hcz	WILD TYPE CYTOCHROME F FROM TURNIP

Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

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