1lk7

Structure of D-Ribose-5-Phosphate Isomerase from in complex with phospho-erythronic acid

Method: X-RAY DIFFRACTION D_max: 87.0 Å Quality: EXCELLENT

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1lk7
沉积日期 deposition_date	2002-04-24
结构标题 title	Structure of D-Ribose-5-Phosphate Isomerase from in complex with phospho-erythronic acid
关键词 keywords	alpha/beta structure, ISOMERASE; ISOMERASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	29.23 Å
回转半径 Rg (电子) rg_electron	28.17 Å
零角强度 I(0) i0	151484000.00
分子量 molecular_weight	101280.0 kDa
排除体积 excluded_volume	128470 Å³
包络体积 envelope_volume	149470 Å³
水化壳体积 shell_volume	42581 Å³
包络直径 envelope_diameter	88.0 Å
壳层 Rg shell_rg	37.11 Å
包络 Rg envelope_rg	28.26 Å
形状 Rg shape_rg	28.16 Å
总 Rg total_rg	29.04 Å
总原子数 total_atoms	7088
残基数 n_residues	916
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	87.0 Å
Rg (实空间) rg_real	29.04 Å
Rg 误差 (实空间) rg_real_error	0.49 Å
I(0) (实空间) i0_real	1.5150e+08
I(0) 误差 (实空间) i0_real_error	1.9120e+06
Rg (倒空间) rg_reciprocal	29.12 Å
I(0) (倒空间) i0_reciprocal	151500000.0000
解质量估计 total_estimate	0.9086
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	40.3 Å
偏度 Skewness skewness	0.056
峰度 Kurtosis kurtosis	-0.587
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	67380000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.958

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	D-Ribose-5-Phosphate Isomerase
分子量 formula_weight	25189.2 kDa
EC 编号 ec_number	5.3.1.6
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	7493

MNVEEMKKIAAKEALKFIEDDMVIGLGTGSTTAYFIKLLGEKLKRGEISDIVGVPTSYQAKLLAIEHDIPIASLDQVDAIDVAVDGADEVDPNLNLIKGRGAALTMEKIIEYRAGTFIVLVDERKLVDYLCQKMPVPIEVIPQAWKAIIEELSIFNAKAELRMGVNKDGPVITDNGNFIIDAKFPRIDDPLDMEIELNTIPGVIENGIFADIADIVIVGTREGVKKLER

来源 Source

来源生物 organism	Pyrococcus horikoshii
NCBI 分类编号 ncbi_taxonomy_id	53953
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	10

Entity 3 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	D-4-PHOSPHOERYTHRONIC ACID
分子量 formula_weight	216.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 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	405

▼

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1lk7a1
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	d1lk7a2
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	d1lk7b1
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	d1lk7b2
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	d1lk7c1
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	d1lk7c2
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	d1lk7d1
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	d1lk7d2
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 (8 domains)

结构域编号 domain_id	1lk7A01
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	1lk7A02
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	1lk7B01
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	1lk7B02
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	1lk7C01
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	1lk7C02
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	1lk7D01
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	1lk7D02
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

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	73.689 Å
晶胞边长 b length_b	114.923 Å
晶胞边长 c length_c	119.578 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	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.2045
R_work r_work	0.2023
R_free r_free	0.2474

fit	/app/data/saxs_computation/lk/1lk7/1lk7.fit
pddf	/app/data/pr_computation/lk/1lk7/1lk7.pr.out
profile	/app/data/saxs_computation/lk/1lk7/1lk7.dat