1vdd

Crystal structure of recombinational repair protein RecR

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Recombination protein recR

Deinococcus radiodurans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 4 IMIDAZOLE × 5 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 8	ZINC ION × 8 IMIDAZOLE × 10 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RECR_DEIRA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–220； UniProt 1–220 Author chain B； PDBConstruct 1–220； UniProt 1–220 Author chain C； PDBConstruct 1–220； UniProt 1–220 Author chain D； PDBConstruct 1–220； UniProt 1–220

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1vdd
Deposition date deposition_date	2004-03-20
Structure title title	Crystal structure of recombinational repair protein RecR
Keywords keywords	Helix-hairpin-helix, zinc finger, toprim, Walker B ATP binding motif, RECOMBINATION; RECOMBINATION
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1vdd__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1vdd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vdd__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.82 Å
Rg (electron density)	33.97 Å
Total Rg	34.69 Å
Atom count	6061
Residues	791
Excluded volume	108470 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vdd__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vdd__assembly_2__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Recombination protein recR
Molecular weight formula_weight	24823.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6126

MKYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVSKPQPPQRPGDEDGADGAAVPASRLEHHHHHH

Source Source

Source organism organism	Deinococcus radiodurans
NCBI taxonomy ID ncbi_taxonomy_id	1299
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

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6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1vdda_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.49 — Recombination protein RecR
Superfamily Superfamily superfamily	e.49.1 — Recombination protein RecR
Family Family family	e.49.1.1 — Recombination protein RecR

Domain ID domain_id	d1vddb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.49 — Recombination protein RecR
Superfamily Superfamily superfamily	e.49.1 — Recombination protein RecR
Family Family family	e.49.1.1 — Recombination protein RecR

Domain ID domain_id	d1vddc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.49 — Recombination protein RecR
Superfamily Superfamily superfamily	e.49.1 — Recombination protein RecR
Family Family family	e.49.1.1 — Recombination protein RecR

Domain ID domain_id	d1vddd_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.49 — Recombination protein RecR
Superfamily Superfamily superfamily	e.49.1 — Recombination protein RecR
Family Family family	e.49.1.1 — Recombination protein RecR

CATH v4.4 (15 domains)

Domain ID domain_id	1vddA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	420 — RecR Domain 1

Domain ID domain_id	1vddA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	1vddA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1vddB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	420 — RecR Domain 1

Domain ID domain_id	1vddB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	1vddB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1vddB04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	1vddC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	420 — RecR Domain 1

Domain ID domain_id	1vddC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	1vddC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1vddC04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	1vddD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	420 — RecR Domain 1

Domain ID domain_id	1vddD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	1vddD03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1vddD04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	240 —

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Unit-cell length a length_a	106.218 Å
Unit-cell length b length_b	121.386 Å
Unit-cell length c length_c	154.993 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	43.390 Å
R factor r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.3010

Crystal structure of recombinational repair protein RecR

1. Protein Identity and Related Structures Protein Identity & Related Structures

Recombination protein recR

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1vdd__assembly_1__model_1

1vdd__assembly_1__model_1 | I(q)

1vdd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (4 domains)

CATH v4.4 (15 domains)

7. Citations (1)

Crystal structure of recombinational repair protein RecR

1. Protein Identity and Related Structures Protein Identity & Related Structures

Recombination protein recR

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1vdd__assembly_1__model_1

1vdd__assembly_1__model_1 | I(q)

1vdd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (4 domains)

CATH v4.4 (15 domains)

7. Citations (1)