1ks2

Crystal Structure Analysis of the rpiA, Structural Genomics, protein EC1268.

Method: X-RAY DIFFRACTION D_max: 83.4 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	1ks2
沉积日期 deposition_date	2002-01-10
结构标题 title	Crystal Structure Analysis of the rpiA, Structural Genomics, protein EC1268.
关键词 keywords	Structural Genomics, Isomerase, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG; Structural Genomics, ISOMERASE
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	24.54 Å
回转半径 Rg (电子) rg_electron	24.01 Å
零角强度 I(0) i0	35872400.00
分子量 molecular_weight	46021.0 kDa
排除体积 excluded_volume	57478 Å³
包络体积 envelope_volume	67200 Å³
水化壳体积 shell_volume	24326 Å³
包络直径 envelope_diameter	86.2 Å
壳层 Rg shell_rg	30.49 Å
包络 Rg envelope_rg	24.22 Å
形状 Rg shape_rg	24.03 Å
总 Rg total_rg	24.69 Å
总原子数 total_atoms	3190
残基数 n_residues	424
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	83.4 Å
Rg (实空间) rg_real	24.67 Å
Rg 误差 (实空间) rg_real_error	0.54 Å
I(0) (实空间) i0_real	3.5870e+07
I(0) 误差 (实空间) i0_real_error	4.8720e+05
Rg (倒空间) rg_reciprocal	24.64 Å
I(0) (倒空间) i0_reciprocal	35870000.0000
解质量估计 total_estimate	0.8578
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	25.2 Å
偏度 Skewness skewness	0.518
峰度 Kurtosis kurtosis	-0.159
角度范围 angular_range	— – 0.3250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13640000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.879; Smooth: 0.934

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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	d1ks2a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.4 — D-ribose-5-phosphate isomerase (RpiA), catalytic domain

结构域编号 domain_id	d1ks2a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.40 — D-ribose-5-phosphate isomerase (RpiA), lid domain
家族 Family family	d.58.40.1 — D-ribose-5-phosphate isomerase (RpiA), lid domain

结构域编号 domain_id	d1ks2b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.4 — D-ribose-5-phosphate isomerase (RpiA), catalytic domain

结构域编号 domain_id	d1ks2b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.40 — D-ribose-5-phosphate isomerase (RpiA), lid domain
家族 Family family	d.58.40.1 — D-ribose-5-phosphate isomerase (RpiA), lid domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1ks2A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1360 —

结构域编号 domain_id	1ks2A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	260 — ACT domain

结构域编号 domain_id	1ks2B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1360 —

结构域编号 domain_id	1ks2B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	260 — ACT domain

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7. 引用文献 (1)

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晶胞边长 a length_a	42.119 Å
晶胞边长 b length_b	42.120 Å
晶胞边长 c length_c	59.429 Å
晶胞夹角 α angle_alpha	89.94 °
晶胞夹角 β angle_beta	100.95 °
晶胞夹角 γ angle_gamma	98.73 °
晶胞分子数 Z z_pdb	2

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

分辨率 resolution	1.500 Å
最低分辨率 resolution_low	34.350 Å
R 因子 r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2370

描述 description	protein EC1268, RPIA
分子量 formula_weight	23164.7 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	3850

Crystal Structure Analysis of the rpiA, Structural Genomics, protein EC1268.

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	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
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	660

fit	/app/data/saxs_computation/ks/1ks2/1ks2.fit
pddf	/app/data/pr_computation/ks/1ks2/1ks2.pr.out
profile	/app/data/saxs_computation/ks/1ks2/1ks2.dat