1wuq

Structure of GTP cyclohydrolase I Complexed with 8-oxo-GTP

Method: X-RAY DIFFRACTION D_max: 107.1 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1wuq
沉积日期 deposition_date	2004-12-08
结构标题 title	Structure of GTP cyclohydrolase I Complexed with 8-oxo-GTP
关键词 keywords	;BETA BARREL, PROTEIN-INHIBITOR COMPLEX, HYDROLASE, PTERIDINE, TETRAHYDROBIOPTERIN, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; HYDROLASE
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	34.00 Å
回转半径 Rg (电子) rg_electron	33.16 Å
零角强度 I(0) i0	183754000.00
分子量 molecular_weight	106710.0 kDa
排除体积 excluded_volume	132940 Å³
包络体积 envelope_volume	184860 Å³
水化壳体积 shell_volume	44743 Å³
包络直径 envelope_diameter	105.8 Å
壳层 Rg shell_rg	41.37 Å
包络 Rg envelope_rg	33.49 Å
形状 Rg shape_rg	33.17 Å
总 Rg total_rg	33.76 Å
总原子数 total_atoms	7460
残基数 n_residues	920
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	107.1 Å
Rg (实空间) rg_real	33.91 Å
Rg 误差 (实空间) rg_real_error	0.77 Å
I(0) (实空间) i0_real	1.8380e+08
I(0) 误差 (实空间) i0_real_error	3.0230e+06
Rg (倒空间) rg_reciprocal	33.97 Å
I(0) (倒空间) i0_reciprocal	183800000.0000
解质量估计 total_estimate	0.9077
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	45.6 Å
偏度 Skewness skewness	0.165
峰度 Kurtosis kurtosis	-0.605
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	27320000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.938

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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	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	7737

MSPGPQSGGQERGSMERKMVELEDTGLTFATEVDLERLQALAAEWLQVIGEDPGREGLLKTPERVAKAWAFLTRGYRQRLEEVVGGAVFPAEGSEMVVVKGVEFYSMCEHHLLPFFGKVHIGYIPDGKILGLSKFARIVDMFARRLQVQERLAVQIAEAIQEVLEPQGVGVVVEGVHLCMMMRGVEKQHSRTVTSAMLGVFRENQKTREEFLSHLRDGTA

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli BL21(DE3)

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 non-polymer

描述 description	8-OXO-GUANOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	539.2 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	277

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6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1wuqa_
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	d1wuqb_
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	d1wuqc_
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	d1wuqd_
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	d1wuqe_
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	1wuqA01
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	1wuqA02
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	1wuqB01
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	1wuqB02
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	1wuqC01
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	1wuqC02
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	1wuqD01
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	1wuqD02
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	1wuqE01
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	1wuqE02
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

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7. 引用文献 (1)

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晶胞边长 a length_a	160.800 Å
晶胞边长 b length_b	110.957 Å
晶胞边长 c length_c	70.463 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	105.53 °
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	2.000 Å
最低分辨率 resolution_low	40.600 Å
R 因子 r_factor	—
R_work r_work	0.2070
R_free r_free	0.2370

fit	/app/data/saxs_computation/wu/1wuq/1wuq.fit
pddf	/app/data/pr_computation/wu/1wuq/1wuq.pr.out
profile	/app/data/saxs_computation/wu/1wuq/1wuq.dat