1fbx

CRYSTAL STRUCTURE OF ZINC-CONTAINING E.COLI GTP CYCLOHYDROLASE I

Method: X-RAY DIFFRACTION D_max: 533.0 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	1fbx
沉积日期 deposition_date	2000-07-17
结构标题 title	CRYSTAL STRUCTURE OF ZINC-CONTAINING E.COLI GTP CYCLOHYDROLASE I
关键词 keywords	HYDROLASE, ALLOSTERIC ENZYME; 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	— Å
回转半径 Rg (电子) rg_electron	125.80 Å
零角强度 I(0) i0	1910180000.00
分子量 molecular_weight	371730.0 kDa
排除体积 excluded_volume	464930 Å³
包络体积 envelope_volume	958950 Å³
水化壳体积 shell_volume	63668 Å³
包络直径 envelope_diameter	367.9 Å
壳层 Rg shell_rg	119.40 Å
包络 Rg envelope_rg	124.00 Å
形状 Rg shape_rg	125.80 Å
总 Rg total_rg	125.80 Å
总原子数 total_atoms	26010
残基数 n_residues	3315
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	533.0 Å
Rg (实空间) rg_real	124.70 Å
Rg 误差 (实空间) rg_real_error	15.48 Å
I(0) (实空间) i0_real	1.9090e+09
I(0) 误差 (实空间) i0_real_error	5.8440e+07
Rg (倒空间) rg_reciprocal	83.57 Å
I(0) (倒空间) i0_reciprocal	1692000000.0000
解质量估计 total_estimate	0.5539
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	4
主峰位置 r_peak_primary	44.4 Å
偏度 Skewness skewness	0.176
峰度 Kurtosis kurtosis	-2.420
角度范围 angular_range	— – 0.0600 Å⁻¹
当前正则化参数 α current_alpha	0.0568
最高正则化参数 α highest_alpha	18170000.0000
实空间数据点数 n_real_points	13
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.002; Oscil: 0.000; Stabil: 0.747; Sysdev: 1.000; Positv: 1.000; Valcen: 0.000; Smooth: 0.000

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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	24733.5 kDa
EC 编号 ec_number	3.5.4.16
来源方法 src_method	man
拷贝数 entity_count	15

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O
原子数 atom_count	26025

PSLSKEAALVHEALVARGLETPLRPPVHEMDNETRKSLIAGHMTEIMQLLNLDLADDSLMETPHRIAKMYVDEIFSGLDYANFPKITLIENKMKVDEMVTVRDITLTSTCEHHFVTIDGKATVAYIPKDSVIGLSKINRIVQFFAQRPQVQERLTQQILIALQTLLGTNNVAVSIDAVHYCVKARGIRDATSATTTTSLGGLFKSSQNTRHEFLRAVRHHN

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
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	15

Entity 3 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	15

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	15

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6. 折叠分类 (SCOP + CATH) 45 domains

SCOP 2.08 (15 domains)

结构域编号 domain_id	d1fbxa_
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	d1fbxb_
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	d1fbxc_
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	d1fbxd_
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	d1fbxe_
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	d1fbxf_
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	d1fbxg_
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	d1fbxh_
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	d1fbxi_
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	d1fbxj_
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	d1fbxk_
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	d1fbxl_
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	d1fbxm_
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	d1fbxn_
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	d1fbxo_
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 (30 domains)

结构域编号 domain_id	1fbxA01
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	1fbxA02
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	1fbxB01
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	1fbxB02
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	1fbxC01
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	1fbxC02
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	1fbxD01
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	1fbxD02
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	1fbxE01
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	1fbxE02
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	1fbxF01
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	1fbxF02
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	1fbxG01
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	1fbxG02
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	1fbxH01
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	1fbxH02
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	1fbxI01
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	1fbxI02
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	1fbxJ01
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	1fbxJ02
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	1fbxK01
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	1fbxK02
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	1fbxL01
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	1fbxL02
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	1fbxM01
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	1fbxM02
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	1fbxN01
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	1fbxN02
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	1fbxO01
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	1fbxO02
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	227.690 Å
晶胞边长 b length_b	314.190 Å
晶胞边长 c length_c	132.570 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	120

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	2.800 Å
最低分辨率 resolution_low	14.980 Å
R 因子 r_factor	0.2020
R_work r_work	0.2020
R_free r_free	0.2510