2hwj

Crystal structure of protein Atu1540 from Agrobacterium tumefaciens

Method: X-RAY DIFFRACTION D_max: 141.2 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	2hwj
沉积日期 deposition_date	2006-08-01
结构标题 title	Crystal structure of protein Atu1540 from Agrobacterium tumefaciens
关键词 keywords	;Agrobacterium tumefaciens, Hypothetical protein, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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	40.97 Å
回转半径 Rg (电子) rg_electron	41.04 Å
零角强度 I(0) i0	268346000.00
分子量 molecular_weight	131820.0 kDa
排除体积 excluded_volume	164230 Å³
包络体积 envelope_volume	223810 Å³
水化壳体积 shell_volume	48456 Å³
包络直径 envelope_diameter	143.1 Å
壳层 Rg shell_rg	43.32 Å
包络 Rg envelope_rg	40.81 Å
形状 Rg shape_rg	41.02 Å
总 Rg total_rg	41.23 Å
总原子数 total_atoms	9260
残基数 n_residues	1133
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	141.2 Å
Rg (实空间) rg_real	41.31 Å
Rg 误差 (实空间) rg_real_error	1.74 Å
I(0) (实空间) i0_real	2.6830e+08
I(0) 误差 (实空间) i0_real_error	5.3460e+06
Rg (倒空间) rg_reciprocal	40.98 Å
I(0) (倒空间) i0_reciprocal	268200000.0000
解质量估计 total_estimate	0.7961
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	39.8 Å
偏度 Skewness skewness	0.559
峰度 Kurtosis kurtosis	-0.413
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22140000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.593; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.767; Smooth: 0.799

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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 (2)

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d2hwja1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.268 — ParB/Sulfiredoxin
超家族 Superfamily superfamily	d.268.1 — ParB/Sulfiredoxin
家族 Family family	d.268.1.3 — Atu1540-like

结构域编号 domain_id	d2hwjb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.268 — ParB/Sulfiredoxin
超家族 Superfamily superfamily	d.268.1 — ParB/Sulfiredoxin
家族 Family family	d.268.1.3 — Atu1540-like

结构域编号 domain_id	d2hwjc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.268 — ParB/Sulfiredoxin
超家族 Superfamily superfamily	d.268.1 — ParB/Sulfiredoxin
家族 Family family	d.268.1.3 — Atu1540-like

结构域编号 domain_id	d2hwjd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.268 — ParB/Sulfiredoxin
超家族 Superfamily superfamily	d.268.1 — ParB/Sulfiredoxin
家族 Family family	d.268.1.3 — Atu1540-like

结构域编号 domain_id	d2hwje_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.268 — ParB/Sulfiredoxin
超家族 Superfamily superfamily	d.268.1 — ParB/Sulfiredoxin
家族 Family family	d.268.1.3 — Atu1540-like

结构域编号 domain_id	d2hwjf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.268 — ParB/Sulfiredoxin
超家族 Superfamily superfamily	d.268.1 — ParB/Sulfiredoxin
家族 Family family	d.268.1.3 — Atu1540-like

CATH v4.4 (12 domains)

结构域编号 domain_id	2hwjA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1530 — Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain
同源超家族 H-superfamily homologous superfamily	10 — Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain

结构域编号 domain_id	2hwjA02
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	10 — Ubiquitin-associated (UBA) domain

结构域编号 domain_id	2hwjB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1530 — Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain
同源超家族 H-superfamily homologous superfamily	10 — Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain

结构域编号 domain_id	2hwjB02
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	10 — Ubiquitin-associated (UBA) domain

结构域编号 domain_id	2hwjC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1530 — Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain
同源超家族 H-superfamily homologous superfamily	10 — Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain

结构域编号 domain_id	2hwjC02
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	10 — Ubiquitin-associated (UBA) domain

结构域编号 domain_id	2hwjD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1530 — Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain
同源超家族 H-superfamily homologous superfamily	10 — Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain

结构域编号 domain_id	2hwjD02
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	10 — Ubiquitin-associated (UBA) domain

结构域编号 domain_id	2hwjE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1530 — Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain
同源超家族 H-superfamily homologous superfamily	10 — Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain

结构域编号 domain_id	2hwjE02
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	10 — Ubiquitin-associated (UBA) domain

结构域编号 domain_id	2hwjF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1530 — Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain
同源超家族 H-superfamily homologous superfamily	10 — Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain

结构域编号 domain_id	2hwjF02
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	10 — Ubiquitin-associated (UBA) domain

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7. 引用文献 (1)

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晶胞边长 a length_a	132.079 Å
晶胞边长 b length_b	173.749 Å
晶胞边长 c length_c	142.077 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	48

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	2.610 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2018
R_work r_work	0.1981
R_free r_free	0.2726

描述 description	Hypothetical protein Atu1540
分子量 formula_weight	23767.5 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	9380

Crystal structure of protein Atu1540 from Agrobacterium tumefaciens

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

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

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

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Agrobacterium tumefaciens str. C58
NCBI 分类编号 ncbi_taxonomy_id	176299
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	95

fit	/app/data/saxs_computation/hw/2hwj/2hwj.fit
pddf	/app/data/pr_computation/hw/2hwj/2hwj.pr.out
profile	/app/data/saxs_computation/hw/2hwj/2hwj.dat