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Description

Title :   NEUTRON CRYSTAL STRUCTURE OF THE RUBREDOXIN MUTANT FROM PYROCOCCUS FURIOSUS

Authors :   T. Chatake, K. Kurihara, I. Tanaka, I. Tsyba, R. Bau, F. E. Jenney, M. W. W N. Niimura

Date :   27 Feb 02 (Deposition) - 27 Aug 02 (Release) - 13 Jul 11 (Revision)

Method :   NEUTRON DIFFRACTION

Resolution :   1.60

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

Keywords :   Rubredoxin, Mutant, Hydrogen, Hydration, Thermostability, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Chatake, K. Kurihara, I. Tanaka, I. Tsyba, R. Bau, F. E. Jenney, M. W. Adams, N. Niimura
A Neutron Crystallographic Analysis Of A Rubredoxin Mutant At 1. 6 A Resolution.
Acta Crystallogr. , Sect. D V. 60 1364 2004
PubMed-ID: 15272158 | Reference-DOI: 10.1107/S090744490401176X

Compounds

Molecule 1 - RUBREDOXIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 32)

Asymmetric Unit (2, 32)

No.	Name	Count	Type	Full Name
1	DOD	31	Ligand/Ion
2	FE	1	Ligand/Ion	FE (III) ION

Biological Unit 1 (0, 0)

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

Sites (0, 0)

(no "Site" information available for 1IU6)

SS Bonds (0, 0)

(no "SS Bond" information available for 1IU6)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1IU6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1IU6)

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBREDOXIN	PS00202	Rubredoxin signature.	RUBR_PYRFU	33-43	1	A:33-42

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBREDOXIN	PS00202	Rubredoxin signature.	RUBR_PYRFU	33-43	1	A:33-42

Exons (0, 0)

(no "Exon" information available for 1IU6)

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
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Chain A from PDB  Type:PROTEIN  Length:52
 aligned with RUBR_PYRFU | P24297 from UniProtKB/Swiss-Prot  Length:54

    Alignment length:52
                                    11        21        31        41        51  
            RUBR_PYRFU    2 AKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKLE 53
               SCOP domains d1iu6a_ A: Rubredoxin                                SCOP domains
               CATH domains 1iu6A00 A:1-52  [code=2.20.28.10, no name defined]   CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eee....hhhhh.....hhhhh...........hhh.eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------RUBREDOXIN ---------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                  1iu6 A  1 AKYVCKICGYIYDEDAGDPDNGVSPGTKFEEIPDDWVCPICGAPKSEFEKLE 52
                                    10        20        30        40        50

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 (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: Rubredoxin-like (572)

Superfamily: Rubredoxin-like (127)

Family: Rubredoxin (85)

Protein domain: Rubredoxin (65)

Pyrococcus furiosus [TaxId: 2261] (25)

d1iu6a_

CATH Domains (1, 1)

Asymmetric 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)

Pyrococcus furiosus. Organism_taxid: 2261. (7)

1iu6A00

A:1-52

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 1IU6)

Gene Ontology (4, 4)

Asymmetric Unit(hide GO term definitions)

Chain A (RUBR_PYRFU | P24297)

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: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.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	RUBR_PYRFU \| P24297	:	1bq8 1bq9 1brf 1caa 1cad 1iu5 1qcv 1rwd 1vcx 1zrp 2pvx 3kyu 3kyv 3kyw 3kyx 3kyy 3ryg 3rz6 3rzt 3ss2 4ar3 4ar4 4ar5 4ar6 4k9f 5ai2 5ai3 5nw3

Related Entries Specified in the PDB File

1iu5	1IU5 CONTAINS X-RAY CRYSTAL STRUCTURE OF THE SAME PROTEIN.