1n3t

Biosynthesis of pteridins. Reaction mechanism of GTP cyclohydrolase I

Method: X-RAY DIFFRACTION D_max: 228.6 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	1n3t
沉积日期 deposition_date	2002-10-29
结构标题 title	Biosynthesis of pteridins. Reaction mechanism of GTP cyclohydrolase I
关键词 keywords	Biosynthesis, folic acid, GTP cyclohydrolase I, tetrahydropterin, pteridines, HYDROLASE; 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	90.59 Å
回转半径 Rg (电子) rg_electron	92.86 Å
零角强度 I(0) i0	2074210000.00
分子量 molecular_weight	378080.0 kDa
排除体积 excluded_volume	470200 Å³
包络体积 envelope_volume	817520 Å³
水化壳体积 shell_volume	75605 Å³
包络直径 envelope_diameter	291.2 Å
壳层 Rg shell_rg	82.05 Å
包络 Rg envelope_rg	91.77 Å
形状 Rg shape_rg	92.85 Å
总 Rg total_rg	92.77 Å
总原子数 total_atoms	26475
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	228.6 Å
Rg (实空间) rg_real	87.13 Å
Rg 误差 (实空间) rg_real_error	1.48 Å
I(0) (实空间) i0_real	2.0100e+09
I(0) 误差 (实空间) i0_real_error	4.7380e+07
Rg (倒空间) rg_reciprocal	80.80 Å
I(0) (倒空间) i0_reciprocal	2014000000.0000
解质量估计 total_estimate	0.6469
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	53.8 Å
偏度 Skewness skewness	0.368
峰度 Kurtosis kurtosis	-1.465
角度范围 angular_range	— – 0.0850 Å⁻¹
当前正则化参数 α current_alpha	0.0335
最高正则化参数 α highest_alpha	56810000.0000
实空间数据点数 n_real_points	18
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.001; Oscil: 0.007; Stabil: 0.764; Sysdev: 1.000; Positv: 1.000; Valcen: 0.209; Smooth: 0.900

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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 (2)

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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	d1n3ta_
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	d1n3tb_
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	d1n3tc_
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	d1n3td_
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	d1n3te_
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	d1n3tf_
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	d1n3tg_
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	d1n3th_
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	d1n3ti_
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	d1n3tj_
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	d1n3tk_
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	d1n3tl_
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	d1n3tm_
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	d1n3tn_
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	d1n3to_
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	1n3tA01
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	1n3tA02
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	1n3tB01
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	1n3tB02
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	1n3tC01
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	1n3tC02
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	1n3tD01
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	1n3tD02
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	1n3tE01
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	1n3tE02
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	1n3tF01
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	1n3tF02
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	1n3tG01
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	1n3tG02
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	1n3tH01
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	1n3tH02
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	1n3tI01
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	1n3tI02
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	1n3tJ01
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	1n3tJ02
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	1n3tK01
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	1n3tK02
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	1n3tL01
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	1n3tL02
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	1n3tM01
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	1n3tM02
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	1n3tN01
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	1n3tN02
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	1n3tO01
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	1n3tO02
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	223.140 Å
晶胞边长 b length_b	317.810 Å
晶胞边长 c length_c	132.150 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	3.200 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1850
R_work r_work	0.1850
R_free r_free	0.2280

描述 description	GTP cyclohydrolase I
分子量 formula_weight	24717.4 kDa
EC 编号 ec_number	3.5.4.16
突变 mutation	C181S
来源方法 src_method	man
拷贝数 entity_count	15

聚合体类型 type	polypeptide(L)
链编号 strand_id	F,G,H,I,J,K,L,M,N,O,A,B,C,D,E
原子数 atom_count	26475

Biosynthesis of pteridins. Reaction mechanism of GTP cyclohydrolase I

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

6. 折叠分类 (SCOP + CATH) 45 domains

SCOP 2.08 (15 domains)

CATH v4.4 (30 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

描述 description	GUANOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	523.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	15

fit	/app/data/saxs_computation/n3/1n3t/1n3t.fit
pddf	/app/data/pr_computation/n3/1n3t/1n3t.pr.out
profile	/app/data/saxs_computation/n3/1n3t/1n3t.dat