1vdd

Crystal structure of recombinational repair protein RecR

Method: X-RAY DIFFRACTION D_max: 105.5 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1vdd
沉积日期 deposition_date	2004-03-20
结构标题 title	Crystal structure of recombinational repair protein RecR
关键词 keywords	Helix-hairpin-helix, zinc finger, toprim, Walker B ATP binding motif, RECOMBINATION; RECOMBINATION
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	34.82 Å
回转半径 Rg (电子) rg_electron	33.97 Å
零角强度 I(0) i0	117274000.00
分子量 molecular_weight	86507.0 kDa
排除体积 excluded_volume	108470 Å³
包络体积 envelope_volume	147550 Å³
水化壳体积 shell_volume	35685 Å³
包络直径 envelope_diameter	107.3 Å
壳层 Rg shell_rg	41.77 Å
包络 Rg envelope_rg	32.34 Å
形状 Rg shape_rg	33.94 Å
总 Rg total_rg	34.69 Å
总原子数 total_atoms	6061
残基数 n_residues	791
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	105.5 Å
Rg (实空间) rg_real	34.66 Å
Rg 误差 (实空间) rg_real_error	0.89 Å
I(0) (实空间) i0_real	1.1730e+08
I(0) 误差 (实空间) i0_real_error	2.0790e+06
Rg (倒空间) rg_reciprocal	34.76 Å
I(0) (倒空间) i0_reciprocal	117300000.0000
解质量估计 total_estimate	0.8955
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	53.9 Å
偏度 Skewness skewness	-0.028
峰度 Kurtosis kurtosis	-0.825
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	20160000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.953

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	Recombination protein recR
分子量 formula_weight	24823.3 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	6126

MKYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVSKPQPPQRPGDEDGADGAAVPASRLEHHHHHH

来源 Source

来源生物 organism	Deinococcus radiodurans
NCBI 分类编号 ncbi_taxonomy_id	1299
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	IMIDAZOLE
分子量 formula_weight	69.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 4 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	65

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6. 折叠分类 (SCOP + CATH) 19 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1vdda_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.49 — Recombination protein RecR
超家族 Superfamily superfamily	e.49.1 — Recombination protein RecR
家族 Family family	e.49.1.1 — Recombination protein RecR

结构域编号 domain_id	d1vddb_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.49 — Recombination protein RecR
超家族 Superfamily superfamily	e.49.1 — Recombination protein RecR
家族 Family family	e.49.1.1 — Recombination protein RecR

结构域编号 domain_id	d1vddc_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.49 — Recombination protein RecR
超家族 Superfamily superfamily	e.49.1 — Recombination protein RecR
家族 Family family	e.49.1.1 — Recombination protein RecR

结构域编号 domain_id	d1vddd_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.49 — Recombination protein RecR
超家族 Superfamily superfamily	e.49.1 — Recombination protein RecR
家族 Family family	e.49.1.1 — Recombination protein RecR

CATH v4.4 (15 domains)

结构域编号 domain_id	1vddA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	420 — RecR Domain 1

结构域编号 domain_id	1vddA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	80 —

结构域编号 domain_id	1vddA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1vddB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	420 — RecR Domain 1

结构域编号 domain_id	1vddB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	80 —

结构域编号 domain_id	1vddB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1vddB04
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	240 —

结构域编号 domain_id	1vddC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	420 — RecR Domain 1

结构域编号 domain_id	1vddC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	80 —

结构域编号 domain_id	1vddC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1vddC04
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	240 —

结构域编号 domain_id	1vddD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	420 — RecR Domain 1

结构域编号 domain_id	1vddD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	80 —

结构域编号 domain_id	1vddD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1vddD04
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	240 —

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7. 引用文献 (1)

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晶胞边长 a length_a	106.218 Å
晶胞边长 b length_b	121.386 Å
晶胞边长 c length_c	154.993 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	32

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	43.390 Å
R 因子 r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.3010

fit	/app/data/saxs_computation/vd/1vdd/1vdd.fit
pddf	/app/data/pr_computation/vd/1vdd/1vdd.pr.out
profile	/app/data/saxs_computation/vd/1vdd/1vdd.dat