1jlh

Human Glucose-6-phosphate Isomerase

Method: X-RAY DIFFRACTION D_max: 190.5 Å Quality: REASONABLE

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	1jlh
沉积日期 deposition_date	2001-07-16
结构标题 title	Human Glucose-6-phosphate Isomerase
关键词 keywords	glycolysis, glyconeogenesis, isomerase; 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	66.25 Å
回转半径 Rg (电子) rg_electron	66.69 Å
零角强度 I(0) i0	864744000.00
分子量 molecular_weight	251490.0 kDa
排除体积 excluded_volume	315320 Å³
包络体积 envelope_volume	455140 Å³
水化壳体积 shell_volume	54543 Å³
包络直径 envelope_diameter	203.3 Å
壳层 Rg shell_rg	76.41 Å
包络 Rg envelope_rg	62.98 Å
形状 Rg shape_rg	66.67 Å
总 Rg total_rg	66.90 Å
总原子数 total_atoms	17748
残基数 n_residues	2224
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	190.5 Å
Rg (实空间) rg_real	67.13 Å
Rg 误差 (实空间) rg_real_error	2.29 Å
I(0) (实空间) i0_real	8.6470e+08
I(0) 误差 (实空间) i0_real_error	1.8840e+07
Rg (倒空间) rg_reciprocal	65.27 Å
I(0) (倒空间) i0_reciprocal	861700000.0000
解质量估计 total_estimate	0.5646
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	39.7 Å
偏度 Skewness skewness	0.168
峰度 Kurtosis kurtosis	-1.437
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	253400000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.012; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.302; Smooth: 0.000

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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)

Entity 1 polymer

描述 description	phosphoglucose isomerase
分子量 formula_weight	63229.9 kDa
EC 编号 ec_number	5.3.1.9
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	19037

MAALTRDPQFQKLQQWYREHRSELNLRRLFDANKDRFNHFSLTLNTNHGHILVDYSKNLVTEDVMRMLVDLAKSRGVEAARERMFNGEKINYTEGRAVLHVALRNRSNTPILVDGKDVMPEVNKVLDKMKSFCQRVRSGDWKGYTGKTITDVINIGIGGSDLGPLMVTEALKPYSSGGPRVWYVSNIDGTHIAKTLAQLNPESSLFIIASKTFTTQETITNAETAKEWFLQAAKDPSAVAKHFVALSTNTTKVKEFGIDPQNMFEFWDWVGGRYSLWSAIGLSIALHVGFDNFEQLLSGAHWMDQHFRTTPLEKNAPVLLALLGIWYINCFGCETHAMLPYDQYLHRFAAYFQQGDMESNGKYITKSGTRVDHQTGPIVWGEPGTNGQHAFYQLIHQGTEMIPCDFLIPVQTQHPIRKGLHHKILLANFLAQTEALMRGKSTEEARKELQAAGKSPEDLERLLPHKVFEGNRPTNSIVFTKLTPFMLGALVAMYEHKIFVQGIIWDINSFDQWGVELGKQLAKKIEPELDGSAQVTSHDASTNGLINFIKQQREARVQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	1289

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1jlha_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.80 — SIS domain
超家族 Superfamily superfamily	c.80.1 — SIS domain
家族 Family family	c.80.1.2 — Phosphoglucose isomerase, PGI

结构域编号 domain_id	d1jlhb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.80 — SIS domain
超家族 Superfamily superfamily	c.80.1 — SIS domain
家族 Family family	c.80.1.2 — Phosphoglucose isomerase, PGI

结构域编号 domain_id	d1jlhc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.80 — SIS domain
超家族 Superfamily superfamily	c.80.1 — SIS domain
家族 Family family	c.80.1.2 — Phosphoglucose isomerase, PGI

结构域编号 domain_id	d1jlhd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.80 — SIS domain
超家族 Superfamily superfamily	c.80.1 — SIS domain
家族 Family family	c.80.1.2 — Phosphoglucose isomerase, PGI

CATH v4.4 (12 domains)

结构域编号 domain_id	1jlhA01
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1jlhA02
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1jlhA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1390 — Phosphoglucose isomerase, C-terminal domain
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1jlhB01
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1jlhB02
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1jlhB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1390 — Phosphoglucose isomerase, C-terminal domain
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1jlhC01
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1jlhC02
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1jlhC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1390 — Phosphoglucose isomerase, C-terminal domain
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1jlhD01
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1jlhD02
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1jlhD03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1390 — Phosphoglucose isomerase, C-terminal domain
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	80.750 Å
晶胞边长 b length_b	108.021 Å
晶胞边长 c length_c	271.073 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	2.100 Å
最低分辨率 resolution_low	22.210 Å
R 因子 r_factor	—
R_work r_work	0.1970
R_free r_free	0.2370

fit	/app/data/saxs_computation/jl/1jlh/1jlh.fit
pddf	/app/data/pr_computation/jl/1jlh/1jlh.pr.out
profile	/app/data/saxs_computation/jl/1jlh/1jlh.dat

Human Glucose-6-phosphate Isomerase

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