1r52

Crystal structure of the bifunctional chorismate synthase from Saccharomyces cerevisiae

Method: X-RAY DIFFRACTION D_max: 99.2 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	1r52
沉积日期 deposition_date	2003-10-09
结构标题 title	Crystal structure of the bifunctional chorismate synthase from Saccharomyces cerevisiae
关键词 keywords	two layers alpha-beta, LYASE; LYASE
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	31.51 Å
回转半径 Rg (电子) rg_electron	30.64 Å
零角强度 I(0) i0	233304000.00
分子量 molecular_weight	121870.0 kDa
排除体积 excluded_volume	152560 Å³
包络体积 envelope_volume	184320 Å³
水化壳体积 shell_volume	48362 Å³
包络直径 envelope_diameter	104.6 Å
壳层 Rg shell_rg	39.20 Å
包络 Rg envelope_rg	30.80 Å
形状 Rg shape_rg	30.67 Å
总 Rg total_rg	31.22 Å
总原子数 total_atoms	8538
残基数 n_residues	1130
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	99.2 Å
Rg (实空间) rg_real	31.41 Å
Rg 误差 (实空间) rg_real_error	0.49 Å
I(0) (实空间) i0_real	2.3330e+08
I(0) 误差 (实空间) i0_real_error	3.7050e+06
Rg (倒空间) rg_reciprocal	31.46 Å
I(0) (倒空间) i0_reciprocal	233300000.0000
解质量估计 total_estimate	0.8914
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	37.7 Å
偏度 Skewness skewness	0.300
峰度 Kurtosis kurtosis	-0.371
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	80670000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; 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) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1r52a_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.258 — Chorismate synthase, AroC
超家族 Superfamily superfamily	d.258.1 — Chorismate synthase, AroC
家族 Family family	d.258.1.1 — Chorismate synthase, AroC

结构域编号 domain_id	d1r52b_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.258 — Chorismate synthase, AroC
超家族 Superfamily superfamily	d.258.1 — Chorismate synthase, AroC
家族 Family family	d.258.1.1 — Chorismate synthase, AroC

结构域编号 domain_id	d1r52c_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.258 — Chorismate synthase, AroC
超家族 Superfamily superfamily	d.258.1 — Chorismate synthase, AroC
家族 Family family	d.258.1.1 — Chorismate synthase, AroC

结构域编号 domain_id	d1r52d_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.258 — Chorismate synthase, AroC
超家族 Superfamily superfamily	d.258.1 — Chorismate synthase, AroC
家族 Family family	d.258.1.1 — Chorismate synthase, AroC

CATH v4.4 (4 domains)

结构域编号 domain_id	1r52A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	150 — Chorismate synthase, AroC fold
同源超家族 H-superfamily homologous superfamily	10 — Chorismate synthase AroC

结构域编号 domain_id	1r52B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	150 — Chorismate synthase, AroC fold
同源超家族 H-superfamily homologous superfamily	10 — Chorismate synthase AroC

结构域编号 domain_id	1r52C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	150 — Chorismate synthase, AroC fold
同源超家族 H-superfamily homologous superfamily	10 — Chorismate synthase AroC

结构域编号 domain_id	1r52D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	150 — Chorismate synthase, AroC fold
同源超家族 H-superfamily homologous superfamily	10 — Chorismate synthase AroC

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7. 引用文献 (1)

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晶胞边长 a length_a	57.816 Å
晶胞边长 b length_b	75.599 Å
晶胞边长 c length_c	91.327 Å
晶胞夹角 α angle_alpha	114.44 °
晶胞夹角 β angle_beta	108.43 °
晶胞夹角 γ angle_gamma	89.98 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.890 Å
最低分辨率 resolution_low	29.750 Å
R 因子 r_factor	0.1898
R_work r_work	0.1879
R_free r_free	0.2239

描述 description	Chorismate synthase
分子量 formula_weight	41721.1 kDa
EC 编号 ec_number	4.2.3.5
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	8636

Crystal structure of the bifunctional chorismate synthase from Saccharomyces cerevisiae

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
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	98

fit	/app/data/saxs_computation/r5/1r52/1r52.fit
pddf	/app/data/pr_computation/r5/1r52/1r52.pr.out
profile	/app/data/saxs_computation/r5/1r52/1r52.dat