1lk5

Structure of the D-Ribose-5-Phosphate Isomerase from Pyrococcus horikoshii

Method: X-RAY DIFFRACTION D_max: 86.7 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	1lk5
沉积日期 deposition_date	2002-04-24
结构标题 title	Structure of the D-Ribose-5-Phosphate Isomerase from Pyrococcus horikoshii
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	29.42 Å
回转半径 Rg (电子) rg_electron	28.28 Å
零角强度 I(0) i0	149052000.00
分子量 molecular_weight	100990.0 kDa
排除体积 excluded_volume	128360 Å³
包络体积 envelope_volume	150860 Å³
水化壳体积 shell_volume	42793 Å³
包络直径 envelope_diameter	90.2 Å
壳层 Rg shell_rg	37.28 Å
包络 Rg envelope_rg	28.39 Å
形状 Rg shape_rg	28.26 Å
总 Rg total_rg	29.16 Å
总原子数 total_atoms	7076
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	86.7 Å
Rg (实空间) rg_real	29.23 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	1.4910e+08
I(0) 误差 (实空间) i0_real_error	2.0170e+06
Rg (倒空间) rg_reciprocal	29.31 Å
I(0) (倒空间) i0_reciprocal	149100000.0000
解质量估计 total_estimate	0.9093
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	40.1 Å
偏度 Skewness skewness	0.062
峰度 Kurtosis kurtosis	-0.589
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	63320000.0000
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: 0.965; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.941

▶

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

▶

5. 实体与聚合体信息 (4)

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	7720

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 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	644

▼

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1lk5a1
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	d1lk5a2
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	d1lk5b1
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	d1lk5b2
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	d1lk5c1
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	d1lk5c2
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	d1lk5d1
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	d1lk5d2
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	1lk5A01
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	1lk5A02
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	1lk5B01
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	1lk5B02
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	1lk5C01
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	1lk5C02
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	1lk5D01
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	1lk5D02
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	73.548 Å
晶胞边长 b length_b	114.932 Å
晶胞边长 c length_c	119.017 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	1.750 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.1920
R_work r_work	0.1910
R_free r_free	0.2150

fit	/app/data/saxs_computation/lk/1lk5/1lk5.fit
pddf	/app/data/pr_computation/lk/1lk5/1lk5.pr.out
profile	/app/data/saxs_computation/lk/1lk5/1lk5.dat