1wm9

Structure of GTP cyclohydrolase I from Thermus thermophilus HB8

Method: X-RAY DIFFRACTION D_max: 107.6 Å Quality: EXCELLENT

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	1wm9
沉积日期 deposition_date	2004-07-05
结构标题 title	Structure of GTP cyclohydrolase I from Thermus thermophilus HB8
关键词 keywords	BETA BARREL, Hydrolase, pteridine, tetrahydrobiopterin, Structural Genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI; 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	34.17 Å
回转半径 Rg (电子) rg_electron	33.31 Å
零角强度 I(0) i0	167121000.00
分子量 molecular_weight	104530.0 kDa
排除体积 excluded_volume	131440 Å³
包络体积 envelope_volume	184760 Å³
水化壳体积 shell_volume	44675 Å³
包络直径 envelope_diameter	107.8 Å
壳层 Rg shell_rg	41.48 Å
包络 Rg envelope_rg	33.54 Å
形状 Rg shape_rg	33.33 Å
总 Rg total_rg	33.88 Å
总原子数 total_atoms	7331
残基数 n_residues	924
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	107.6 Å
Rg (实空间) rg_real	34.07 Å
Rg 误差 (实空间) rg_real_error	0.60 Å
I(0) (实空间) i0_real	1.6710e+08
I(0) 误差 (实空间) i0_real_error	2.3600e+06
Rg (倒空间) rg_reciprocal	34.13 Å
I(0) (倒空间) i0_reciprocal	167100000.0000
解质量估计 total_estimate	0.9062
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	46.8 Å
偏度 Skewness skewness	0.176
峰度 Kurtosis kurtosis	-0.596
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	41580000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.930

▶

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

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	GTP cyclohydrolase I
分子量 formula_weight	24571.3 kDa
EC 编号 ec_number	3.5.4.16
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E
原子数 atom_count	7677

MSPGPQSGGQERGSMERKMVELEDTGLTFATEVDLERLQALAAEWLQVIGEDPGREGLLKTPERVAKAWAFLTRGYRQRLEEVVGGAVFPAEGSEMVVVKGVEFYSMCEHHLLPFFGKVHIGYIPDGKILGLSKFARIVDMFARRLQVQERLAVQIAEAIQEVLEPQGVGVVVEGVHLCMMMRGVEKQHSRTVTSAMLGVFRENQKTREEFLSHLRDGTA

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	300852
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	5

Entity 3 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	346

▼

6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1wm9a1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.1 — GTP cyclohydrolase I

结构域编号 domain_id	d1wm9b_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.1 — GTP cyclohydrolase I

结构域编号 domain_id	d1wm9c_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.1 — GTP cyclohydrolase I

结构域编号 domain_id	d1wm9d_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.1 — GTP cyclohydrolase I

结构域编号 domain_id	d1wm9e_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.1 — GTP cyclohydrolase I

CATH v4.4 (10 domains)

结构域编号 domain_id	1wm9A01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

结构域编号 domain_id	1wm9A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1130 — GTP Cyclohydrolase I, domain 2
同源超家族 H-superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

结构域编号 domain_id	1wm9B01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

结构域编号 domain_id	1wm9B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1130 — GTP Cyclohydrolase I, domain 2
同源超家族 H-superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

结构域编号 domain_id	1wm9C01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

结构域编号 domain_id	1wm9C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1130 — GTP Cyclohydrolase I, domain 2
同源超家族 H-superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

结构域编号 domain_id	1wm9D01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

结构域编号 domain_id	1wm9D02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1130 — GTP Cyclohydrolase I, domain 2
同源超家族 H-superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

结构域编号 domain_id	1wm9E01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

结构域编号 domain_id	1wm9E02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1130 — GTP Cyclohydrolase I, domain 2
同源超家族 H-superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	160.220 Å
晶胞边长 b length_b	110.477 Å
晶胞边长 c length_c	70.650 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	105.27 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	20

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2130
R_work r_work	0.2080
R_free r_free	0.2610

fit	/app/data/saxs_computation/wm/1wm9/1wm9.fit
pddf	/app/data/pr_computation/wm/1wm9/1wm9.pr.out
profile	/app/data/saxs_computation/wm/1wm9/1wm9.dat