3SID - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

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, AZIDE ADDUCT AT 50% OCCUPANCY

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

Date :   17 Jun 11 (Deposition) - 31 Aug 11 (Release) - 12 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Ferritin-Like Superfamily, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. B. Cooley, D. J. Arp, P. A. Karplus
Symerythrin Structures At Atomic Resolution And The Origins Of Rubrerythrins And The Ferritin-Like Superfamily.
J. Mol. Biol. V. 413 177 2011
PubMed-ID: 21872605 | Reference-DOI: 10.1016/J.JMB.2011.08.019

Molecule 1 - SYMERYTHRIN
	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	:	CYANELLE 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 (2, 6)

No.	Name	Count	Type	Full Name
1	AZI	2	Ligand/Ion	AZIDE ION
2	FE	4	Ligand/Ion	FE (III) ION

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:71 , GLU A:128 , GLU A:162 , HIS A:165 , HOH A:183 , FE A:201 , AZI A:300	BINDING SITE FOR RESIDUE FE A 200
2	AC2	SOFTWARE	GLU A:37 , GLU A:40 , GLU A:71 , GLU A:131 , GLU A:162 , HOH A:183 , FE A:200 , HOH A:204 , AZI A:300	BINDING SITE FOR RESIDUE FE A 201
3	AC3	SOFTWARE	GLU A:40 , GLU A:71 , VAL A:127 , GLU A:128 , GLU A:131 , GLU A:162 , HOH A:183 , FE A:200 , FE A:201 , HOH A:204	BINDING SITE FOR RESIDUE AZI A 300
4	AC4	SOFTWARE	GLU B:37 , GLU B:40 , GLU B:71 , GLU B:131 , GLU B:162 , HOH B:181 , HOH B:198 , FE B:201 , AZI B:300	BINDING SITE FOR RESIDUE FE B 200
5	AC5	SOFTWARE	GLU B:71 , GLU B:128 , GLU B:162 , HIS B:165 , HOH B:181 , FE B:200 , AZI B:300	BINDING SITE FOR RESIDUE FE B 201
6	AC6	SOFTWARE	GLU B:40 , GLU B:71 , VAL B:127 , GLU B:128 , GLU B:131 , GLU B:162 , HOH B:181 , HOH B:198 , FE B:200 , FE B:201	BINDING SITE FOR RESIDUE AZI B 300

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

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

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

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 3SID)

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:177
 aligned with YCX8_CYAPA | P48329 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:177
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       
           YCX8_CYAPA     4 NYNQEDFMGLDRFFQDAVSHNNTDANAASSIEVEMYECDCMYPTFAEIARRSGQPEIGAMFDAIAKEEGMHAQLLTKLYSELEVKDSAETLEAKRLVSTIESQIDAVASDSRGLRRALETALEVETIESQKTYPAFAKLAAEQGNMEVATAFEAIVKSETKHANWVKRALENLLEVA 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
                 3sid A   4 NYNQEDFMGLDRFFQDAVSHNNTDANAASSIEVEMYECDCMYPTFAEIARRSGQPEIGAMFDAIAKEEGMHAQLLTKLYSELEVKDSAETLEAKRLVSTIESQIDAVASDSRGLRRALETALEVETIESQKTYPAFAKLAAEQGNMEVATAFEAIVKSETKHANWVKRALENLLEVA 180
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

Chain B from PDB  Type:PROTEIN  Length:177
 aligned with YCX8_CYAPA | P48329 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:177
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       
           YCX8_CYAPA     4 NYNQEDFMGLDRFFQDAVSHNNTDANAASSIEVEMYECDCMYPTFAEIARRSGQPEIGAMFDAIAKEEGMHAQLLTKLYSELEVKDSAETLEAKRLVSTIESQIDAVASDSRGLRRALETALEVETIESQKTYPAFAKLAAEQGNMEVATAFEAIVKSETKHANWVKRALENLLEVA 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: B:21-180 UniProt: 21-180                                                                                                                     PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sid B   4 NYNQEDFMGLDRFFQDAVSHNNTDANAASSIEVEMYECDCMYPTFAEIARRSGQPEIGAMFDAIAKEEGMHAQLLTKLYSELEVKDSAETLEAKRLVSTIESQIDAVASDSRGLRRALETALEVETIESQKTYPAFAKLAAEQGNMEVATAFEAIVKSETKHANWVKRALENLLEVA 180
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

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 3SID)

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

(no "Pfam Domain" information available for 3SID)

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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		AZI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3sid)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3sid
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	YCX8_CYAPA \| P48329
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	YCX8_CYAPA \| P48329
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	YCX8_CYAPA \| P48329	:	3qhb 3qhc

3qhb	OXIDIZED SYMERYTHRIN FROM C. PARADOXA
3qhc	SYMERYTHRIN FROM C. PARADOXA, REDUCED WITH DITHIONITE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File