2dxb

Recombinant thiocyanate hydrolase comprising partially-modified cobalt centers

Method: X-RAY DIFFRACTION D_max: 176.7 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2dxb
沉积日期 deposition_date	2006-08-25
结构标题 title	Recombinant thiocyanate hydrolase comprising partially-modified cobalt centers
关键词 keywords	;hydrolase, cobalt, metalloprotein, sulfenic acid, sulfinic acid, nitrile hydratase, thiocyanate, carbonyl sulfide, claw setting, protein, enzyme, complex, model complex, non-corrin, post-translational modification, sulfenate, sulfinate ;; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	59.37 Å
回转半径 Rg (电子) rg_electron	59.56 Å
零角强度 I(0) i0	2825390000.00
分子量 molecular_weight	446650.0 kDa
排除体积 excluded_volume	557940 Å³
包络体积 envelope_volume	744660 Å³
水化壳体积 shell_volume	102800 Å³
包络直径 envelope_diameter	192.2 Å
壳层 Rg shell_rg	62.32 Å
包络 Rg envelope_rg	58.17 Å
形状 Rg shape_rg	59.55 Å
总 Rg total_rg	59.65 Å
总原子数 total_atoms	31450
残基数 n_residues	3892
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

▼

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

最大尺寸 Dmax dmax	176.7 Å
Rg (实空间) rg_real	59.54 Å
Rg 误差 (实空间) rg_real_error	1.78 Å
I(0) (实空间) i0_real	2.8250e+09
I(0) 误差 (实空间) i0_real_error	5.4750e+07
Rg (倒空间) rg_reciprocal	59.18 Å
I(0) (倒空间) i0_reciprocal	2824000000.0000
解质量估计 total_estimate	0.8325
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	54.4 Å
偏度 Skewness skewness	0.290
峰度 Kurtosis kurtosis	-0.786
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	125900000.0000
实空间数据点数 n_real_points	27
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.000

▶

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

▶

5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	Thiocyanate hydrolase subunit alpha
分子量 formula_weight	14507.2 kDa
EC 编号 ec_number	3.5.5.8
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D,G,J,M,P,S,V
原子数 atom_count	34391

MSDSHHKPVWDRTHHAKMATGIGDPQCFKGMAGKSKFNVGDRVRIKDLPDLFYTRTMTYTRGATGTIVRLVYESPAAEDEAFGNEENVEWFYSIVFAQKDLWPEYSDTFANDTLETEIPERYLEKA

来源 Source

来源生物 organism	Thiobacillus thioparus
NCBI 分类编号 ncbi_taxonomy_id	931
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Thiocyanate hydrolase subunit beta
分子量 formula_weight	18065.5 kDa
EC 编号 ec_number	3.5.5.8
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,E,H,K,N,Q,T,W

MSSSIREEVHRHLGTVALMQPALHQQTHAPAPTEITHTLFRAYTRVPHDVGGEADVPIEYHEKEEEIWELNTFATCECLAWRGVWTAEERRRKQNCDVGQTVYLGMPYYGRWLLTAARILVDKQFVTLTELHNKIVEMRERVASGQGLGEYLPPKAK

来源 Source

来源生物 organism	Thiobacillus thioparus
NCBI 分类编号 ncbi_taxonomy_id	931
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

描述 description	Thiocyanate hydrolase subunit gamma
分子量 formula_weight	27619.4 kDa
EC 编号 ec_number	3.5.5.8
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,F,I,L,O,R,U,X

MSADHDHDHDHDHDHKPAPMVEEVSDFEILEMAVRELAIEKGLFSAEDHRVWKDYVHTLGPLPAARLVAKAWLDPEYKKLCIEDGVEASKAVGVNWVTSPPTQFGTPSDYCNLRVLADSPTLKHVVVCTLCSCYPRPILGQSPEWYRSPNYRRRLVRWPRQVLAEFGLQLPSEVQIRVADSNQKTRYIVMPVRPEGTDGWTEDQLAEIVTRDCLIGVAVPKPGITVNAKRPVLKANRPVHHDH

来源 Source

来源生物 organism	Thiobacillus thioparus
NCBI 分类编号 ncbi_taxonomy_id	931
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 non-polymer

描述 description	COBALT (III) ION
分子量 formula_weight	58.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 5 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 6 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	2941

▼

6. 折叠分类 (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

结构域编号 domain_id	2dxbA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	2dxbB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	472 — Cyclin A; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Nitrile hydratase, beta subunit

结构域编号 domain_id	2dxbC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	330 — Nitrile Hydratase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma

结构域编号 domain_id	2dxbD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	2dxbE00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	472 — Cyclin A; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Nitrile hydratase, beta subunit

结构域编号 domain_id	2dxbF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	330 — Nitrile Hydratase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma

结构域编号 domain_id	2dxbG00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	2dxbH00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	472 — Cyclin A; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Nitrile hydratase, beta subunit

结构域编号 domain_id	2dxbI00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	330 — Nitrile Hydratase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma

结构域编号 domain_id	2dxbJ00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	2dxbK00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	472 — Cyclin A; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Nitrile hydratase, beta subunit

结构域编号 domain_id	2dxbL00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	330 — Nitrile Hydratase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma

结构域编号 domain_id	2dxbM00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	2dxbN00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	472 — Cyclin A; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Nitrile hydratase, beta subunit

结构域编号 domain_id	2dxbO00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	330 — Nitrile Hydratase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma

结构域编号 domain_id	2dxbP00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	2dxbQ00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	472 — Cyclin A; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Nitrile hydratase, beta subunit

结构域编号 domain_id	2dxbR00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	330 — Nitrile Hydratase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma

结构域编号 domain_id	2dxbS00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	2dxbT00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	472 — Cyclin A; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Nitrile hydratase, beta subunit

结构域编号 domain_id	2dxbU00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	330 — Nitrile Hydratase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma

结构域编号 domain_id	2dxbV00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	2dxbW00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	472 — Cyclin A; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Nitrile hydratase, beta subunit

结构域编号 domain_id	2dxbX00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	330 — Nitrile Hydratase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	114.874 Å
晶胞边长 b length_b	245.141 Å
晶胞边长 c length_c	244.653 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	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.250 Å
最低分辨率 resolution_low	49.410 Å
R 因子 r_factor	0.1710
R_work r_work	0.1710
R_free r_free	0.1980

fit	/app/data/saxs_computation/dx/2dxb/2dxb.fit
pddf	/app/data/pr_computation/dx/2dxb/2dxb.pr.out
profile	/app/data/saxs_computation/dx/2dxb/2dxb.dat

Recombinant thiocyanate hydrolase comprising partially-modified cobalt centers

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 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)