1wu2

Crystal Structure of molybdopterin biosynthesis moeA protein from Pyrococcus horikoshii OT3

Method: X-RAY DIFFRACTION D_max: 117.3 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1wu2
沉积日期 deposition_date	2004-11-30
结构标题 title	Crystal Structure of molybdopterin biosynthesis moeA protein from Pyrococcus horikoshii OT3
关键词 keywords	moeA protein, structural genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, BIOSYNTHETIC PROTEIN; STRUCTURAL GENOMICS,BIOSYNTHETIC PROTEIN
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	33.02 Å
回转半径 Rg (电子) rg_electron	32.63 Å
零角强度 I(0) i0	104580000.00
分子量 molecular_weight	85327.0 kDa
排除体积 excluded_volume	108510 Å³
包络体积 envelope_volume	141620 Å³
水化壳体积 shell_volume	38047 Å³
包络直径 envelope_diameter	124.0 Å
壳层 Rg shell_rg	37.22 Å
包络 Rg envelope_rg	33.22 Å
形状 Rg shape_rg	32.63 Å
总 Rg total_rg	33.00 Å
总原子数 total_atoms	5978
残基数 n_residues	750
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	117.3 Å
Rg (实空间) rg_real	33.41 Å
Rg 误差 (实空间) rg_real_error	1.26 Å
I(0) (实空间) i0_real	1.0460e+08
I(0) 误差 (实空间) i0_real_error	1.6830e+06
Rg (倒空间) rg_reciprocal	33.24 Å
I(0) (倒空间) i0_reciprocal	104600000.0000
解质量估计 total_estimate	0.8070
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	36.7 Å
偏度 Skewness skewness	0.674
峰度 Kurtosis kurtosis	0.196
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12920000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.634; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.860; Smooth: 0.726

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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) 14 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1wu2a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.85 — beta-clip
超家族 Superfamily superfamily	b.85.6 — MoeA C-terminal domain-like
家族 Family family	b.85.6.1 — MoeA C-terminal domain-like

结构域编号 domain_id	d1wu2a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.103 — MoeA N-terminal region -like
超家族 Superfamily superfamily	b.103.1 — MoeA N-terminal region -like
家族 Family family	b.103.1.1 — MoeA N-terminal region -like

结构域编号 domain_id	d1wu2a3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.57 — Molybdenum cofactor biosynthesis proteins
超家族 Superfamily superfamily	c.57.1 — Molybdenum cofactor biosynthesis proteins
家族 Family family	c.57.1.2 — MoeA central domain-like

结构域编号 domain_id	d1wu2b1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.85 — beta-clip
超家族 Superfamily superfamily	b.85.6 — MoeA C-terminal domain-like
家族 Family family	b.85.6.1 — MoeA C-terminal domain-like

结构域编号 domain_id	d1wu2b2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.103 — MoeA N-terminal region -like
超家族 Superfamily superfamily	b.103.1 — MoeA N-terminal region -like
家族 Family family	b.103.1.1 — MoeA N-terminal region -like

结构域编号 domain_id	d1wu2b3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.57 — Molybdenum cofactor biosynthesis proteins
超家族 Superfamily superfamily	c.57.1 — Molybdenum cofactor biosynthesis proteins
家族 Family family	c.57.1.2 — MoeA central domain-like

CATH v4.4 (8 domains)

结构域编号 domain_id	1wu2A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	980 — Molybdenum Cofactor Biosythetic Enzyme; Chain A
同源超家族 H-superfamily homologous superfamily	10 — MoaB/Mog-like domain

结构域编号 domain_id	1wu2A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	105 — Molybdopterin biosynthesis moea protein, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Molybdopterin biosynthesis moea protein, domain 2

结构域编号 domain_id	1wu2A03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	190 — Molybdopterin biosynthesis moeA protein; domain 3
同源超家族 H-superfamily homologous superfamily	11 — Molybdopterin biosynthesis moea protein, domain 3.

结构域编号 domain_id	1wu2A04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	340 — Beta-clip
同源超家族 H-superfamily homologous superfamily	10 — MoeA, C-terminal, domain IV

结构域编号 domain_id	1wu2B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	980 — Molybdenum Cofactor Biosythetic Enzyme; Chain A
同源超家族 H-superfamily homologous superfamily	10 — MoaB/Mog-like domain

结构域编号 domain_id	1wu2B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	105 — Molybdopterin biosynthesis moea protein, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Molybdopterin biosynthesis moea protein, domain 2

结构域编号 domain_id	1wu2B03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	190 — Molybdopterin biosynthesis moeA protein; domain 3
同源超家族 H-superfamily homologous superfamily	11 — Molybdopterin biosynthesis moea protein, domain 3.

结构域编号 domain_id	1wu2B04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	340 — Beta-clip
同源超家族 H-superfamily homologous superfamily	10 — MoeA, C-terminal, domain IV

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7. 引用文献 (1)

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晶胞边长 a length_a	173.149 Å
晶胞边长 b length_b	65.912 Å
晶胞边长 c length_c	76.684 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	102.17 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.300 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2357
R_work r_work	0.2332
R_free r_free	0.2823

描述 description	molybdopterin biosynthesis moeA protein
分子量 formula_weight	44479.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	6401

Crystal Structure of molybdopterin biosynthesis moeA protein from Pyrococcus horikoshii OT3

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 water

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Pyrococcus horikoshii
NCBI 分类编号 ncbi_taxonomy_id	53953
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	423

fit	/app/data/saxs_computation/wu/1wu2/1wu2.fit
pddf	/app/data/pr_computation/wu/1wu2/1wu2.pr.out
profile	/app/data/saxs_computation/wu/1wu2/1wu2.dat