1VDD - JenaLib

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Title :   CRYSTAL STRUCTURE OF RECOMBINATIONAL REPAIR PROTEIN RECR

Authors :   B. I. Lee, K. H. Kim, S. W. Suh

Date :   20 Mar 04 (Deposition) - 18 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Helix-Hairpin-Helix, Zinc Finger, Toprim, Walker B Atp Binding Motif, Recombination (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. I. Lee, K. H. Kim, S. J. Park, S. H. Eom, H. K. Song, S. W. Suh
Ring-Shaped Architecture Of Recr: Implications For Its Role In Homologous Recombinational Dna Repair
Embo J. V. 23 2029 2004
PubMed-ID: 15116069 | Reference-DOI: 10.1038/SJ.EMBOJ.7600222
(for further references see the PDB file header)

Molecule 1 - RECOMBINATION PROTEIN RECR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-199
	Gene	:	RECR
	Organism Scientific	:	DEINOCOCCUS RADIODURANS
	Organism Taxid	:	1299

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (2x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	IMD	5	Ligand/Ion	IMIDAZOLE
2	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	IMD	5	Ligand/Ion	IMIDAZOLE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 10)

No.	Name	Count	Type	Full Name
1	IMD	10	Ligand/Ion	IMIDAZOLE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:57 , CYS A:60 , CYS A:69 , CYS A:72	BINDING SITE FOR RESIDUE ZN A 230
2	AC2	SOFTWARE	CYS B:57 , CYS B:60 , CYS B:69 , CYS B:72	BINDING SITE FOR RESIDUE ZN B 231
3	AC3	SOFTWARE	CYS C:57 , CYS C:60 , CYS C:69 , CYS C:72	BINDING SITE FOR RESIDUE ZN C 232
4	AC4	SOFTWARE	CYS D:57 , CYS D:60 , CYS D:69 , CYS D:72	BINDING SITE FOR RESIDUE ZN D 233
5	AC5	SOFTWARE	HIS B:108 , GLU D:34	BINDING SITE FOR RESIDUE IMD D 2023
6	AC6	SOFTWARE	GLU C:67 , ASP D:65 , ALA D:66	BINDING SITE FOR RESIDUE IMD C 2024
7	AC7	SOFTWARE	GLU B:34 , LYS C:125 , GLU D:87 , HIS D:108	BINDING SITE FOR RESIDUE IMD B 2025
8	AC8	SOFTWARE	ASP C:53 , ASP C:65 , GLU D:67	BINDING SITE FOR RESIDUE IMD D 2026
9	AC9	SOFTWARE	GLU A:87 , HIS A:108 , MET A:114 , GLU C:34	BINDING SITE FOR RESIDUE IMD A 2027

Asymmetric Unit

No.	Residues
1	C:69	-	C:72

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

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECR	PS01300	RecR protein signature.	RECR_DEIRA	57-78	4	A:57-78 B:57-78 C:57-78 D:57-78
2	TOPRIM	PS50880	Toprim domain profile.	RECR_DEIRA	80-173	4	A:80-173 B:80-173 C:80-173 D:80-173

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECR	PS01300	RecR protein signature.	RECR_DEIRA	57-78	4	A:57-78 B:57-78 C:57-78 D:57-78
2	TOPRIM	PS50880	Toprim domain profile.	RECR_DEIRA	80-173	4	A:80-173 B:80-173 C:80-173 D:80-173

Biological Unit 2 (2, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECR	PS01300	RecR protein signature.	RECR_DEIRA	57-78	8	A:57-78 B:57-78 C:57-78 D:57-78
2	TOPRIM	PS50880	Toprim domain profile.	RECR_DEIRA	80-173	8	A:80-173 B:80-173 C:80-173 D:80-173

(no "Exon" information available for 1VDD)

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:199
 aligned with RECR_DEIRA | Q9ZNA2 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         
           RECR_DEIRA     1 MKYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVSKP 199
               SCOP domains d1vdda_ A: Recombination protein RecR                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhee......ee....hhhhhh......eeeee.hhhhhhhh........eeee.....hhhhh.......hhhhhhhh....eeee....hhhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------RECR  PDB: A:57-78    -TOPRIM  PDB: A:80-173 UniProt: 80-173                                                         -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vdd A   1 MKYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVSKP 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:198
 aligned with RECR_DEIRA | Q9ZNA2 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
           RECR_DEIRA     2 KYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVSKP 199
               SCOP domains d1vddb_ B: Recombination protein RecR                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhee......ee....hhhhhh......eeeee.hhhhhhhhhhhh....eeee.....hhhhh.hhhhh.hhhhhhhh....eeee....hhhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------RECR  PDB: B:57-78    -TOPRIM  PDB: B:80-173 UniProt: 80-173                                                         -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vdd B   2 KYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVSKP 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain C from PDB  Type:PROTEIN  Length:196
 aligned with RECR_DEIRA | Q9ZNA2 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:196
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191      
           RECR_DEIRA     2 KYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVS 197
               SCOP domains d1vddc_ C: Recombination protein RecR                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhee......ee....hhhhhh......eeeee.hhhhhhhhhh......eeee...........hhhhh....hhhhh...eeeeee.....hhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------RECR  PDB: C:57-78    -TOPRIM  PDB: C:80-173 UniProt: 80-173                                                         ------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vdd C   2 KYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVS 197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain D from PDB  Type:PROTEIN  Length:198
 aligned with RECR_DEIRA | Q9ZNA2 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
           RECR_DEIRA     2 KYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVSKP 199
               SCOP domains d1vddd_ D: Recombination protein RecR                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhee......ee....hhhhhh...eeeeeeee..hhhhhhhhh.....eeeee.....hhhhh.hhhhh.hhhhhhhh....eeee....hhhhhhhhhhhhhhhhhhh.eeee..............hhhhhhhhhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------RECR  PDB: D:57-78    -TOPRIM  PDB: D:80-173 UniProt: 80-173                                                         -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vdd D   2 KYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVSKP 199
                                    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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: Recombination protein RecR (4)

Superfamily: Recombination protein RecR (4)

Family: Recombination protein RecR (4)

Protein domain: Recombination protein RecR (4)

Deinococcus radiodurans [TaxId: 1299] (2)

1a	d1vdda_	A:
1b	d1vddb_	B:
1c	d1vddc_	C:
1d	d1vddd_	D:

(no "CATH Domain" information available for 1VDD)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RECR_DEIRA | Q9ZNA2)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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.
	GO:0006302	double-strand break repair	The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.

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Description

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Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

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