1YUZ - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   PARTIALLY REDUCED STATE OF NIGERYTHRIN

Authors :   R. B. Iyer, R. Silaghi-Dumitrescu, D. M. Kurtz, W. N. Lanzilotta

Date :   14 Feb 05 (Deposition) - 21 Jun 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   Rubrythrin, Rubredoxin, Hemerythrin, Electron Transfer, Diiron Center, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. B. Iyer, R. Silaghi-Dumitrescu, D. M. Kurtz, W. N. Lanzilotta
High-Resolution Crystal Structures Of Desulfovibrio Vulgari (Hildenborough) Nigerythrin: Facile, Redox-Dependent Iron Movement, Domain Interface Variability, And Peroxidase Activity In The Rubrerythrins.
J. Biol. Inorg. Chem. V. 10 407 2005
PubMed-ID: 15895271 | Reference-DOI: 10.1007/S00775-005-0650-8

Molecule 1 - NIGERYTHRIN
	Atcc	:	29579
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	NGR
	Organism Scientific	:	DESULFOVIBRIO VULGARIS SUBSP. VULGARIS
	Organism Taxid	:	882
	Strain	:	HILDENBOROUGH

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:40 , GLU A:73 , GLU A:118 , GLU A:149 , FE2 A:302 , HOH A:471	BINDING SITE FOR RESIDUE FE A 301
2	AC2	SOFTWARE	GLU A:73 , GLU A:115 , GLU A:149 , HIS A:152 , FE A:301 , HOH A:471	BINDING SITE FOR RESIDUE FE2 A 302
3	AC3	SOFTWARE	CYS A:174 , CYS A:177 , CYS A:189 , CYS A:192	BINDING SITE FOR RESIDUE FE A 303
4	AC4	SOFTWARE	GLU B:40 , GLU B:73 , GLU B:118 , GLU B:149 , FE2 B:302 , HOH B:501	BINDING SITE FOR RESIDUE FE B 301
5	AC5	SOFTWARE	GLU B:73 , GLU B:115 , GLU B:149 , HIS B:152 , FE B:301 , HOH B:501	BINDING SITE FOR RESIDUE FE2 B 302
6	AC6	SOFTWARE	CYS B:174 , CYS B:177 , CYS B:189 , CYS B:192	BINDING SITE FOR RESIDUE FE B 303

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

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

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FERRITIN_LIKE	PS50905	Ferritin-like diiron domain profile.	NIGY_DESVH	23-168	2	A:23-168 B:23-168
2	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	NIGY_DESVH	169-202	2	A:169-202 B:169-202

(no "Exon" information available for 1YUZ)

Asymmetric/Biological 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:200
 aligned with NIGY_DESVH | P30820 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
           NIGY_DESVH     1 MKVRAQVPTVKNATNFNMVADSKTAVGSTLENLKAAIAGETGAHAKYTAFAKAAREQGYEQIARLFEATAAAELIHIGLEYALVAEMEPGYEKPTVAAPSAYSCDLNLISGANGEIYETSDMYPAFIRKAQEEGNSKAVHVFTRAKLAESVHAERYLAAYNDIDAPDDDKFHLCPICGYIHKGEDFEKCPICFRPKDTFTAY 202
               SCOP domains ----------------------d1yuza1 A:23-157 Nigerythrin, N-terminal domain                                                                                        ---------d1yuza2 A:167-202                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------1yuzA02 A:165-202                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........--....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee......eee............hhhhheee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------FERRITIN_LIKE  PDB: A:23-168 UniProt: 23-168                                                                                                      RUBREDOXIN_LIKE  PDB: A:169-202    PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yuz A   1 MKVRAQVPTVKNATNFNMVADSKTAVGSTLENLKAAIAGETGAHAKYTAFAKAAREQGYEQIARLFEATAAAELIHIGLEYALVAEMEPGYEKPTV--PSAYSCDLNLISGANGEIYETSDMYPAFIRKAQEEGNSKAVHVFTRAKLAESVHAERYLAAYNDIDAPDDDKFHLCPICGYIHKGEDFEKCPICFRPKDTFTAY 202
                                    10        20        30        40        50        60        70        80        90     | 100       110       120       130       140       150       160       170       180       190       200  
                                                                                                                          96 99

Chain B from PDB  Type:PROTEIN  Length:202
 aligned with NIGY_DESVH | P30820 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
           NIGY_DESVH     1 MKVRAQVPTVKNATNFNMVADSKTAVGSTLENLKAAIAGETGAHAKYTAFAKAAREQGYEQIARLFEATAAAELIHIGLEYALVAEMEPGYEKPTVAAPSAYSCDLNLISGANGEIYETSDMYPAFIRKAQEEGNSKAVHVFTRAKLAESVHAERYLAAYNDIDAPDDDKFHLCPICGYIHKGEDFEKCPICFRPKDTFTAY 202
               SCOP domains ----------------------d1yuzb1 B:23-157 Nigerythrin, N-terminal domain                                                                                        ---------d1yuzb2 B:167-202                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------1yuzB02 B:165-202                      CATH domains
           Pfam domains (1) ------------------------------Rubrerythrin-1yuzB01 B:31-160                                                                                                     ------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------------------------Rubrerythrin-1yuzB02 B:31-160                                                                                                     ------------------------------------------ Pfam domains (2)
         Sec.struct. author ...........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee......eee............hhhhheee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------FERRITIN_LIKE  PDB: B:23-168 UniProt: 23-168                                                                                                      RUBREDOXIN_LIKE  PDB: B:169-202    PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yuz B   1 MKVRAQVPTVKNATNFNMVADSKTAVGSTLENLKAAIAGETGAHAKYTAFAKAAREQGYEQIARLFEATAAAELIHIGLEYALVAEMEPGYEKPTVAAPSAYSCDLNLISGANGEIYETSDMYPAFIRKAQEEGNSKAVHVFTRAKLAESVHAERYLAAYNDIDAPDDDKFHLCPICGYIHKGEDFEKCPICFRPKDTFTAY 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

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/Biological 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: Nigerythrin, N-terminal domain (3)

Desulfovibrio vulgaris [TaxId: 881] (3)

1a	d1yuza1	A:23-157
1b	d1yuzb1	B:23-157

Class: Small proteins (3458)

Fold: Rubredoxin-like (572)

Superfamily: Rubredoxin-like (127)

Family: Rubredoxin (85)

Protein domain: Nigerythrin, C-terminal domain (3)

Desulfovibrio vulgaris [TaxId: 881] (3)

2a	d1yuza2	A:167-202
2b	d1yuzb2	B:167-202

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Single Sheet (341)

Topology: Rubrerythrin, domain 2 (145)

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

Vulgaris str (Desulfovibrio vulgaris subsp) (8)

1a	1yuzA02	A:165-202
1b	1yuzB02	B:165-202

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Rubrerythrin (18)

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

1a	Rubrerythrin-1yuzB01	B:31-160
1b	Rubrerythrin-1yuzB02	B:31-160

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NIGY_DESVH | P30820)

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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological 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
		FE	[ 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 ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1yuz)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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
	1yuz
		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
	NIGY_DESVH \| P30820
		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
	NIGY_DESVH \| P30820
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	NIGY_DESVH \| P30820	:	1yux 1yv1

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 (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (1, 2)

Pfam Domains (1, 2)

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