1LKP - JenaLib

Biol.Unit 1 - manually

Asym.Unit - manually

Asymmetric Unit

Asym. Unit - sites

Biological Unit 1

Biol. Unit 1 - sites

Biological Unit 2

collapse

expand

Biol.Unit 1 - manually (Jmol Viewer)

Asym.Unit - manually (Jmol Viewer)

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)

Description

Title :   CRYSTAL STRUCTURE OF DESULFOVIBRIO VULGARIS RUBRERYTHRIN ALL-IRON(II) FORM, AZIDE ADDUCT

Authors :   S. Jin, D. M. Kurtz Jr. , Z. J. Liu, J. Rose, B. C. Wang

Date :   25 Apr 02 (Deposition) - 18 Sep 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.64

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)
Biol. Unit 2: A  (4x)

Keywords :   Rubrerythrin, Reduced Form, Azide Adduct, Diiron, Four-Helix Bundle, Rubredoxin-Like, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Jin, D. M. Kurtz Jr. , Z. J. Liu, J. Rose, B. C. Wang
X-Ray Crystal Structures Of Reduced Rubrerythrin And Its Azide Adduct: A Structure-Based Mechanism For A Non-Heme Diiron Peroxidase
J. Am. Chem. Soc. V. 124 9845 2002
PubMed-ID: 12175244 | Reference-DOI: 10.1021/JA026587U

Compounds

Molecule 1 - RUBRERYTHRIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	'BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	DESULFOVIBRIO VULGARIS
	Organism Taxid	:	881
	Other Details	:	ALL-IRON (II) FORM

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A
Biological Unit 2 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 5)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	AZI	2	Ligand/Ion	AZIDE ION
2	FE2	3	Ligand/Ion	FE (II) ION

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	AZI	4	Ligand/Ion	AZIDE ION
2	FE2	6	Ligand/Ion	FE (II) ION

Biological Unit 2 (2, 20)

No.	Name	Count	Type	Full Name
1	AZI	8	Ligand/Ion	AZIDE ION
2	FE2	12	Ligand/Ion	FE (II) ION

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:20 , GLU A:53 , GLU A:94 , GLU A:97 , GLU A:128 , FE2 A:600 , FE2 A:601	BINDING SITE FOR RESIDUE AZI A 2000
2	AC2	SOFTWARE	ASP A:82 , HIS A:84 , ALA A:85 , HOH A:2159	BINDING SITE FOR RESIDUE AZI A 2001
3	AC3	SOFTWARE	GLU A:53 , GLU A:94 , GLU A:128 , HIS A:131 , AZI A:2000	BINDING SITE FOR RESIDUE FE2 A 600
4	AC4	SOFTWARE	GLU A:20 , GLU A:53 , HIS A:56 , GLU A:128 , AZI A:2000	BINDING SITE FOR RESIDUE FE2 A 601
5	AC5	SOFTWARE	CYS A:158 , CYS A:161 , CYS A:174 , CYS A:177	BINDING SITE FOR RESIDUE FE2 A 401

SS Bonds (0, 0)

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

Cis Peptide Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	Gly A:78	-	Ile A:79

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FERRITIN_LIKE	PS50905	Ferritin-like diiron domain profile.	RUBY_DESVH	3-146	1	A:3-146
2	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBY_DESVH	153-187	1	A:153-187

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FERRITIN_LIKE	PS50905	Ferritin-like diiron domain profile.	RUBY_DESVH	3-146	2	A:3-146
2	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBY_DESVH	153-187	2	A:153-187

Biological Unit 2 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FERRITIN_LIKE	PS50905	Ferritin-like diiron domain profile.	RUBY_DESVH	3-146	4	A:3-146
2	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBY_DESVH	153-187	4	A:153-187

Exons (0, 0)

(no "Exon" information available for 1LKP)

Sequences/Alignments

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:190
 aligned with RUBY_DESVH | P24931 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:190
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
           RUBY_DESVH     2 KSLKGSRTEKNILTAFAGESQARNRYNYFGGQAKKDGFVQISDIFAETADQEREHAKRLFKFLEGGDLEIVAAFPAGIIADTHANLIASAAGEHHEYTEMYPSFARIAREEGYEEIARVFASIAVAEEFHEKRFLDFARNIKEGRVFLREQATKWRCRNCGYVHEGTGAPELCPACAHPKAHFELLGINW 191
               SCOP domains d1lkpa1 A:2-147 Rubrerythrin, N-terminal domain                                                                                                   d1lkpa2 A:148-191                            SCOP domains
               CATH domains 1lkpA01 A:2-146  [code=1.20.1260.10, no name defined]                                                                                            1lkpA02 A:147-191                             CATH domains
               Pfam domains ---------Rubrerythrin-1lkpA01 A:11-139                                                                                                    ---------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee.....eeeeee..........hhh.eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -FERRITIN_LIKE  PDB: A:3-146 UniProt: 3-146                                                                                                      ------RUBREDOXIN_LIKE  PDB: A:153-187    ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lkp A   2 KSLKGSRTEKNILTAFAGESQARNRYNYFGGQAKKDGFVQISDIFAETADQEREHAKRLFKFLEGGDLEIVAAFPAGIIADTHANLIASAAGEHHEYTEMYPSFARIAREEGYEEIARVFASIAVAEEFHEKRFLDFARNIKEGRVFLREQATKWRCRNCGYVHEGTGAPELCPACAHPKAHFELLGINW 191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Ferritin-like (533)

Superfamily: Ferritin-like (489)

Family: Ferritin (232)

Protein domain: Rubrerythrin, N-terminal domain (12)

Desulfovibrio vulgaris [TaxId: 881] (10)

d1lkpa1

A:2-147

Class: Small proteins (3458)

Fold: Rubredoxin-like (572)

Superfamily: Rubredoxin-like (127)

Family: Rubredoxin (85)

Protein domain: Rubrerythrin, C-terminal domain (12)

Desulfovibrio vulgaris [TaxId: 881] (10)

d1lkpa2

A:148-191

CATH Domains (2, 2)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Ferritin; (180)

Homologous Superfamily: [code=1.20.1260.10, no name defined] (180)

Desulfovibrio vulgaris. Organism_taxid: 881. (5)

1lkpA01

A:2-146

Class: Mainly Beta (13760)

Architecture: Single Sheet (341)

Topology: Rubrerythrin, domain 2 (145)

Homologous Superfamily: [code=2.20.28.10, no name defined] (77)

Desulfovibrio vulgaris. Organism_taxid: 881. (5)

1lkpA02

A:147-191

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Rubrerythrin (18)

Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303) (10)

Rubrerythrin-1lkpA01

A:11-139

Gene Ontology (6, 6)

Asymmetric Unit(hide GO term definitions)

Chain A (RUBY_DESVH | P24931)

molecular function
	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.
	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:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Visualization

Interactive Views

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 ]
		FE2	[ 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 ]

	Cis Peptide Bonds
		Gly A:78 - Ile A:79	[ RasMol ]

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

Still Images

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)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1lkp
		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
	RUBY_DESVH \| P24931
		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

Analysis Tools

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
	RUBY_DESVH \| P24931
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	RUBY_DESVH \| P24931	:	1b71 1dvb 1jyb 1lkm 1lko 1qyb 1ryt 1s2z 1s30

Related Entries Specified in the PDB File

1lkm	SAME PROTEIN CRYSTALIZED UNDER DIFFERENT CONDITIONS
1lko	SAME PROTEIN CRYSTALIZED UNDER DIFFERENT CONDITIONS