2CVF - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE RADB RECOMBINASE

Authors :   T. Akiba, N. Ishii, N. Rashid, M. Morikawa, T. Imanaka, K. Harata

Date :   03 Jun 05 (Deposition) - 09 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Radb, Filament Formation, Homologous Recombination, Atpase Domain, Hyperthermophile, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Akiba, N. Ishii, N. Rashid, M. Morikawa, T. Imanaka, K. Harata
Structure Of Radb Recombinase From A Hyperthermophilic Archaeon, Thermococcus Kodakaraensis Kod1: An Implication For The Formation Of A Near-7-Fold Helical Assembly
Nucleic Acids Res. V. 33 3412 2005
PubMed-ID: 15956102 | Reference-DOI: 10.1093/NAR/GKI662
(for further references see the PDB file header)

Molecule 1 - DNA REPAIR AND RECOMBINATION PROTEIN RADB
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-8C
	Expression System Strain	:	HMS174(DE)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PK-REC
	Organism Scientific	:	THERMOCOCCUS KODAKARENSIS
	Organism Taxid	:	311400

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2CVF)

(no "Site" information available for 2CVF)

(no "SS Bond" information available for 2CVF)

Asymmetric Unit

No.	Residues
1	Thr A:84	-	Pro A:85
2	Asp A:112	-	Ser A:113
3	Asp B:112	-	Ser B:113

(no "SAP(SNP)/Variant" information available for 2CVF)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECA_2	PS50162	RecA family profile 1.	RADB_THEKO	1-155	2	A:1-155 B:1-155

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECA_2	PS50162	RecA family profile 1.	RADB_THEKO	1-155	1	A:1-155 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECA_2	PS50162	RecA family profile 1.	RADB_THEKO	1-155	1	- B:1-155

(no "Exon" information available for 2CVF)

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:220
 aligned with RADB_THEKO | P95547 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
           RADB_THEKO     1 MLSTGTKSLDSLLGGGFAPGVLTQVYGPYASGKTTLALQTGLLSGKKVAYVDTEGGFSPERLVQMAETRGLNPEEALSRFILFTPSDFKEQRRVIGSLKKTVDSNFALVVVDSITAHYRAEENRSGLIAELSRQLQVLLWIARKHNIPVIVINQVHFDSRTEMTKPVAEQTLGYRCKDILRLDKLPKPGLRVAVLERHRFRPEGLMAYFRITERGIEDVE 220
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhh..........eee....hhhhhhhhhhhh....eeee........hhhhhhhhhh.....hhhh.eeee......hhhhhhhhhhhh.......eee............hhhhhhhh.hhhhhhhhhhhhh....eeeee.............hhhhhhhhh.....eee......eeee...........eee.eee..eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RECA_2  PDB: A:1-155 UniProt: 1-155                                                                                                                        ----------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cvf A   1 MLSTGTKSLDSLLGGGFAPGVLTQVYGPYASGKTTLALQTGLLSGKKVAYVDTEGGFSPERLVQMAETRGLNPEEALSRFILFTPSDFKEQRRVIGSLKKTVDSNFALVVVDSITAHYRAEENRSGLIAELSRQLQVLLWIARKHNIPVIVINQVHFDSRTEMTKPVAEQTLGYRCKDILRLDKLPKPGLRVAVLERHRFRPEGLMAYFRITERGIEDVE 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with RADB_THEKO | P95547 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
           RADB_THEKO     1 MLSTGTKSLDSLLGGGFAPGVLTQVYGPYASGKTTLALQTGLLSGKKVAYVDTEGGFSPERLVQMAETRGLNPEEALSRFILFTPSDFKEQRRVIGSLKKTVDSNFALVVVDSITAHYRAEENRSGLIAELSRQLQVLLWIARKHNIPVIVINQVHFDSRTEMTKPVAEQTLGYRCKDILRLDKLPKPGLRVAVLERHRFRPEGLMAYFRITERGIEDVE 220
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh................hhhhhhhhhhhhhh..eeeee.........hhhhhhhhhh.hhhhhhhheeee....hhhhhhhhhhhh......eeeeee..............hhhhhhhhhhhhhhhhhhhh.........eee.......ee....hhhhhh...eeeee......eeeee..........eeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RECA_2  PDB: B:1-155 UniProt: 1-155                                                                                                                        ----------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cvf B   1 MLSTGTKSLDSLLGGGFAPGVLTQVYGPYASGKTTLALQTGLLSGKKVAYVDTEGGFSPERLVQMAETRGLNPEEALSRFILFTPSDFKEQRRVIGSLKKTVDSNFALVVVDSITAHYRAEENRSGLIAELSRQLQVLLWIARKHNIPVIVINQVHFDSRTEMTKPVAEQTLGYRCKDILRLDKLPKPGLRVAVLERHRFRPEGLMAYFRITERGIEDVE 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

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 2CVF)

(no "CATH Domain" information available for 2CVF)

(no "Pfam Domain" information available for 2CVF)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RADB_THEKO | P95547)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008094	DNA-dependent ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
	GO:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

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
(no "Ligands, Modified Residues, Ions" information available for 2cvf)

	Sites
(no "Sites" information available for 2cvf)

	Cis Peptide Bonds
		Asp A:112 - Ser A:113	[ RasMol ]
		Asp B:112 - Ser B:113	[ RasMol ]
		Thr A:84 - Pro A:85	[ RasMol ]

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 \| Biol. Unit 1 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
	2cvf
		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
	RADB_THEKO \| P95547
		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
	RADB_THEKO \| P95547
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	RADB_THEKO \| P95547	:	2cvh

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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 (9, 9)

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