8p4i

Cyanide dihydratase from Bacillus pumilus C1

Method: ELECTRON MICROSCOPY D_max: 192.3 Å Quality: REASONABLE

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	8p4i
沉积日期 deposition_date	2023-05-22
最后修订 last_revision	2023-08-16
结构标题 title	Cyanide dihydratase from Bacillus pumilus C1
关键词 keywords	Cyanide degrading enzyme, HYDROLASE; HYDROLASE
实验方法 method	ELECTRON MICROSCOPY

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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	58.75 Å
回转半径 Rg (电子) rg_electron	58.40 Å
零角强度 I(0) i0	5203670000.00
分子量 molecular_weight	610140.0 kDa
排除体积 excluded_volume	761970 Å³
包络体积 envelope_volume	1146200 Å³
水化壳体积 shell_volume	157250 Å³
包络直径 envelope_diameter	212.3 Å
壳层 Rg shell_rg	66.07 Å
包络 Rg envelope_rg	56.87 Å
形状 Rg shape_rg	58.42 Å
总 Rg total_rg	58.51 Å
总原子数 total_atoms	42976
残基数 n_residues	5389
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	192.3 Å
Rg (实空间) rg_real	58.52 Å
Rg 误差 (实空间) rg_real_error	1.30 Å
I(0) (实空间) i0_real	5.2040e+09
I(0) 误差 (实空间) i0_real_error	1.0540e+08
Rg (倒空间) rg_reciprocal	58.92 Å
I(0) (倒空间) i0_reciprocal	5207000000.0000
解质量估计 total_estimate	0.6198
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	78.4 Å
偏度 Skewness skewness	0.268
峰度 Kurtosis kurtosis	-0.228
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	724400000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.779; Stabil: 1.000; Sysdev: 0.009; Positv: 1.000; Valcen: 0.973; Smooth: 0.714

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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 (1)

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6. 折叠分类 (SCOP + CATH) 17 domains

CATH v4.4 (17 domains)

结构域编号 domain_id	8p4iB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iJ01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iK01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iL01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iM01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iN01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iO01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iP01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iQ01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iR01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iS01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	8p4iU01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	3.83 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	120943

描述 description	Cyanide dihydratase
分子量 formula_weight	35941.4 kDa
来源方法 src_method	man
拷贝数 entity_count	17

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,U
原子数 atom_count	42976

Cyanide dihydratase from Bacillus pumilus C1

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 17 domains

CATH v4.4 (17 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Bacillus pumilus
NCBI 分类编号 ncbi_taxonomy_id	1408
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/p4/8p4i/8p4i.fit
pddf	/app/data/pr_computation/p4/8p4i/8p4i.pr.out
profile	/app/data/saxs_computation/p4/8p4i/8p4i.dat