3QHB - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF OXIDIZED SYMERYTHRIN FROM CYANOPHORA PARADOXA

Authors :   R. B. Cooley, D. J. Arp, P. A. Karplus

Date :   25 Jan 11 (Deposition) - 25 May 11 (Release) - 01 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

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

Keywords :   Four-Helix Bundle, Carboxylate Bridged-Diiron, Ferritin-Like Superfamily, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. B. Cooley, T. W. Rhoads, D. J. Arp, P. A. Karplus
A Diiron Protein Autogenerates A Valine-Phenylalanine Cross-Link.
Science V. 332 929 2011
PubMed-ID: 21596985 | Reference-DOI: 10.1126/SCIENCE.1205687

Molecule 1 - SYMERYTHRIN
	Cellular Location	:	PLASTID; CYANELLE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7-7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ORF180
	Organism Scientific	:	CYANOPHORA PARADOXA
	Organism Taxid	:	2762
	Synonym	:	ORF180

		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, 4)

No.	Name	Count	Type	Full Name
1	FE	4	Ligand/Ion	FE (III) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:71 , GLU A:128 , GLU A:162 , HIS A:165 , FE A:181 , HOH A:190	BINDING SITE FOR RESIDUE FE A 182
2	AC2	SOFTWARE	GLU A:37 , GLU A:40 , GLU A:71 , GLU A:131 , GLU A:162 , FE A:182 , HOH A:190	BINDING SITE FOR RESIDUE FE A 181
3	AC3	SOFTWARE	GLU B:71 , GLU B:128 , GLU B:162 , HIS B:165 , FE B:181 , HOH B:192	BINDING SITE FOR RESIDUE FE B 182
4	AC4	SOFTWARE	GLU B:37 , GLU B:40 , GLU B:71 , GLU B:131 , GLU B:162 , FE B:182 , HOH B:192	BINDING SITE FOR RESIDUE FE B 181

(no "SS Bond" information available for 3QHB)

(no "Cis Peptide Bond" information available for 3QHB)

(no "SAP(SNP)/Variant" information available for 3QHB)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FERRITIN_LIKE	PS50905	Ferritin-like diiron domain profile.	YCX8_CYAPA	21-180	2	A:21-180 B:21-180

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FERRITIN_LIKE	PS50905	Ferritin-like diiron domain profile.	YCX8_CYAPA	21-180	1	A:21-180 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FERRITIN_LIKE	PS50905	Ferritin-like diiron domain profile.	YCX8_CYAPA	21-180	1	- B:21-180

(no "Exon" information available for 3QHB)

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:179
 aligned with YCX8_CYAPA | P48329 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171         
           YCX8_CYAPA     2 GLNYNQEDFMGLDRFFQDAVSHNNTDANAASSIEVEMYECDCMYPTFAEIARRSGQPEIGAMFDAIAKEEGMHAQLLTKLYSELEVKDSAETLEAKRLVSTIESQIDAVASDSRGLRRALETALEVETIESQKTYPAFAKLAAEQGNMEVATAFEAIVKSETKHANWVKRALENLLEVA 180
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------FERRITIN_LIKE  PDB: A:21-180 UniProt: 21-180                                                                                                                     PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qhb A   2 GLNYNQEDFMGLDRFFQDAVSHNNTDANAASSIEVEMYECDCMYPTFAEIARRSGQPEIGAMFDAIAKEEGMHAQLLTKLYSELEVKDSAETLEAKRLVSTIESQIDAVASDSRGLRRALETALEVETIESQKTYPAFAKLAAEQGNMEVATAFEAIVKSETKHANWVKRALENLLEVA 180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Chain B from PDB  Type:PROTEIN  Length:179
 aligned with YCX8_CYAPA | P48329 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171         
           YCX8_CYAPA     2 GLNYNQEDFMGLDRFFQDAVSHNNTDANAASSIEVEMYECDCMYPTFAEIARRSGQPEIGAMFDAIAKEEGMHAQLLTKLYSELEVKDSAETLEAKRLVSTIESQIDAVASDSRGLRRALETALEVETIESQKTYPAFAKLAAEQGNMEVATAFEAIVKSETKHANWVKRALENLLEVA 180
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------Rubrerythrin-3qhbB01 B:31-173                                                                                                                  ------- Pfam domains (1)
           Pfam domains (2) -----------------------------Rubrerythrin-3qhbB02 B:31-173                                                                                                                  ------- Pfam domains (2)
           Pfam domains (3) -----------------------------Rubrerythrin-3qhbB03 B:31-173                                                                                                                  ------- Pfam domains (3)
           Pfam domains (4) -----------------------------Rubrerythrin-3qhbB04 B:31-173                                                                                                                  ------- Pfam domains (4)
         Sec.struct. author .......hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------FERRITIN_LIKE  PDB: B:21-180 UniProt: 21-180                                                                                                                     PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qhb B   2 GLNYNQEDFMGLDRFFQDAVSHNNTDANAASSIEVEMYECDCMYPTFAEIARRSGQPEIGAMFDAIAKEEGMHAQLLTKLYSELEVKDSAETLEAKRLVSTIESQIDAVASDSRGLRRALETALEVETIESQKTYPAFAKLAAEQGNMEVATAFEAIVKSETKHANWVKRALENLLEVA 180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

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 '\|'

(no "SCOP Domain" information available for 3QHB)

(no "CATH Domain" information available for 3QHB)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Rubrerythrin (18)

Cyanophora paradoxa (1)

1a	Rubrerythrin-3qhbB01	B:31-173
1b	Rubrerythrin-3qhbB02	B:31-173
1c	Rubrerythrin-3qhbB03	B:31-173
1d	Rubrerythrin-3qhbB04	B:31-173

Asymmetric Unit(hide GO term definitions)

Chain A,B (YCX8_CYAPA | P48329)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
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.
cellular component
	GO:0009842	cyanelle	A plastid that contains unstacked, phycobilisome-bearing thylakoid membranes and is surrounded by a double membrane with a peptidoglycan layer in the intermembrane space between the two envelope membranes. Cyanelles are characteristic of algae in the class Glaucophyta, and may represent an ancestral form of plastid.
	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.

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Description

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Ligands, Modified Residues, Ions (1, 4)

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