1T9P - JenaLib

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)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF V44A, G45P CP RUBREDOXIN

Authors :   I. Y. Park, M. K. Eidsness, I. J. Lin, E. B. Gebel, B. Youn, J. L. Harley, T. E. Machonkin, R. O. Frederick, J. L. Markley, E. T. Smith, T. Ichiye, C. Kang

Date :   18 May 04 (Deposition) - 05 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

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

Reference :   I. Y. Park, M. K. Eidsness, I. J. Lin, E. B. Gebel, B. Youn, J. L. Harley, T. E. Machonkin, R. O. Frederick, J. L. Markley, E. T. Smith, T. Ichiye, C. Kang
Crystallographic Studies Of V44 Mutants Of Clostridium Pasteurianum Rubredoxin: Effects Of Side-Chain Size On Reduction Potential.
Proteins V. 57 618 2004
PubMed-ID: 15382226 | Reference-DOI: 10.1002/PROT.20243
(for further references see the PDB file header)

Molecule 1 - RUBREDOXIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	CLOSTRIDIUM PASTEURIANUM
	Organism Taxid	:	1501
	Synonym	:	RD

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	FE	3	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

Biological Unit 3 (0, 0)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:6 , CYS A:9 , CYS A:39 , CYS A:42	BINDING SITE FOR RESIDUE FE A 55
2	AC2	SOFTWARE	CYS B:106 , CYS B:109 , CYS B:139 , CYS B:142	BINDING SITE FOR RESIDUE FE B 155
3	AC3	SOFTWARE	CYS C:206 , CYS C:209 , CYS C:239 , CYS C:242	BINDING SITE FOR RESIDUE FE C 255

(no "SS Bond" information available for 1T9P)

(no "Cis Peptide Bond" information available for 1T9P)

(no "SAP(SNP)/Variant" information available for 1T9P)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBR_CLOPA	1-52	3	A:1-52 B:101-152 C:201-252
2	RUBREDOXIN	PS00202	Rubredoxin signature.	RUBR_CLOPA	33-43	3	A:33-43 B:133-143 C:233-243

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBR_CLOPA	1-52	1	A:1-52 - -
2	RUBREDOXIN	PS00202	Rubredoxin signature.	RUBR_CLOPA	33-43	1	A:33-43 - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBR_CLOPA	1-52	1	- B:101-152 -
2	RUBREDOXIN	PS00202	Rubredoxin signature.	RUBR_CLOPA	33-43	1	- B:133-143 -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBR_CLOPA	1-52	1	- - C:201-252
2	RUBREDOXIN	PS00202	Rubredoxin signature.	RUBR_CLOPA	33-43	1	- - C:233-243

(no "Exon" information available for 1T9P)

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:54
 aligned with RUBR_CLOPA | P00268 from UniProtKB/Swiss-Prot  Length:54

    Alignment length:54
                                    10        20        30        40        50    
           RUBR_CLOPA     1 MKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEVEE  54
               SCOP domains d1t9pa_ A: Rubredoxin                                  SCOP domains
               CATH domains 1t9pA00 A:1-54  [code=2.20.28.10, no name defined]     CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee.....ee.....hhhhh.....hhhhh...........hhh.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: A:1-52 UniProt: 1-52          -- PROSITE (1)
                PROSITE (2) --------------------------------RUBREDOXIN ----------- PROSITE (2)
                 Transcript ------------------------------------------------------ Transcript
                 1t9p A   1 MKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGAPKDQFEEVEE  54
                                    10        20        30        40        50

Chain B from PDB  Type:PROTEIN  Length:54
 aligned with RUBR_CLOPA | P00268 from UniProtKB/Swiss-Prot  Length:54

    Alignment length:54
                                    10        20        30        40        50    
           RUBR_CLOPA     1 MKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEVEE  54
               SCOP domains d1t9pb_ B: Rubredoxin                                  SCOP domains
               CATH domains 1t9pB00 B:101-154  [code=2.20.28.10, no name defined]  CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee.....ee.....hhhhh.....hhhhh...........hhh.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: B:101-152 UniProt: 1-52       -- PROSITE (1)
                PROSITE (2) --------------------------------RUBREDOXIN ----------- PROSITE (2)
                 Transcript ------------------------------------------------------ Transcript
                 1t9p B 101 MKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGAPKDQFEEVEE 154
                                   110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:54
 aligned with RUBR_CLOPA | P00268 from UniProtKB/Swiss-Prot  Length:54

    Alignment length:54
                                    10        20        30        40        50    
           RUBR_CLOPA     1 MKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEVEE  54
               SCOP domains d1t9pc_ C: Rubredoxin                                  SCOP domains
               CATH domains 1t9pC00 C:201-254  [code=2.20.28.10, no name defined]  CATH domains
           Pfam domains (1) --Rubredoxin-1t9pC01 C:203-249                   ----- Pfam domains (1)
           Pfam domains (2) --Rubredoxin-1t9pC02 C:203-249                   ----- Pfam domains (2)
           Pfam domains (3) --Rubredoxin-1t9pC03 C:203-249                   ----- Pfam domains (3)
         Sec.struct. author ...eee.....ee.....hhhhh.....hhhhh...........hhh.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: C:201-252 UniProt: 1-52       -- PROSITE (1)
                PROSITE (2) --------------------------------RUBREDOXIN ----------- PROSITE (2)
                 Transcript ------------------------------------------------------ Transcript
                 1t9p C 201 MKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGAPKDQFEEVEE 254
                                   210       220       230       240       250

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 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)

Clostridium pasteurianum [TaxId: 1501] (23)

1a	d1t9pa_	A:
1b	d1t9pb_	B:
1c	d1t9pc_	C:

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)

Clostridium pasteurianum. Organism_taxid: 1501. (14)

1a	1t9pA00	A:1-54
1b	1t9pB00	B:101-154
1c	1t9pC00	C:201-254

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Rubredoxin (46)

Family: Rubredoxin (29)

Clostridium pasteurianum (10)

1a	Rubredoxin-1t9pC01	C:203-249
1b	Rubredoxin-1t9pC02	C:203-249
1c	Rubredoxin-1t9pC03	C:203-249

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (RUBR_CLOPA | P00268)

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.

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
		FE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1t9p)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ 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 \| Biol. Unit 3 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
	1t9p
		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
	RUBR_CLOPA \| P00268
		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
	RUBR_CLOPA \| P00268
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1t9o	CRYSTAL STRUCTURE OF V44G CP RUBREDOXIN
1t9q	CRYSTAL STRUCTURE OF V44L CP RUBREDOXIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (1, 3)

Gene Ontology (4, 4)

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