1iri

Crystal structure of human autocrine motility factor complexed with an inhibitor

Method: X-RAY DIFFRACTION D_max: 152.1 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	1iri
沉积日期 deposition_date	2001-10-08
结构标题 title	Crystal structure of human autocrine motility factor complexed with an inhibitor
关键词 keywords	cytokine, 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	47.15 Å
回转半径 Rg (电子) rg_electron	47.03 Å
零角强度 I(0) i0	914710000.00
分子量 molecular_weight	252820.0 kDa
排除体积 excluded_volume	316830 Å³
包络体积 envelope_volume	399990 Å³
水化壳体积 shell_volume	69975 Å³
包络直径 envelope_diameter	156.6 Å
壳层 Rg shell_rg	51.92 Å
包络 Rg envelope_rg	46.21 Å
形状 Rg shape_rg	47.02 Å
总 Rg total_rg	47.24 Å
总原子数 total_atoms	17828
残基数 n_residues	2228
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	152.1 Å
Rg (实空间) rg_real	47.35 Å
Rg 误差 (实空间) rg_real_error	1.22 Å
I(0) (实空间) i0_real	9.1470e+08
I(0) 误差 (实空间) i0_real_error	1.7330e+07
Rg (倒空间) rg_reciprocal	47.15 Å
I(0) (倒空间) i0_reciprocal	914500000.0000
解质量估计 total_estimate	0.7955
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	41.5 Å
偏度 Skewness skewness	0.352
峰度 Kurtosis kurtosis	-0.724
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	327300000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.788; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; 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 (3)

Entity 1 polymer

描述 description	autocrine motility factor
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	18264

MAALTRDPQFQKLQQWYREHRSELNLRRLFDANKDRFNHFSLTLNTNHGHILVDYSKNLVTEDVMRMLVDLAKSRGVEAARERMFNGEKINYTEGRAVLHVALRNRSNTPILVDGKDVMPEVNKVLDKMKSFCQRVRSGDWKGYTGKTITDVINIGIGGSDLGPLMVTEALKPYSSGGPRVWYVSNIDGTHIAKTLAQLNPESSLFIIASKTFTTQETITNAETAKEWFLQAAKDPSAVAKHFVALSTNTTKVKEFGIDPQNMFEFWDWVGGRYSLWSAIGLSIALHVGFDNFEQLLSGAHWMDQHFRTTPLEKNAPVLLALLGIWYINCFGCETHAMLPYDQYLHRFAAYFQQGDMESNGKYITKSGTRVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQTQHPIRKGLHHKILLANFLAQTEALMRGKSTEEARKELQAAGKSPEDLERLLPHKVFEGNRPTNSIVFTKLTPFMLGALVAMYEHKIFVQGIIWDINSFDQWGVELGKQLAKKIEPELDGSAQVTSHDASTNGLINFIKQQREARVQ

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

Entity 2 non-polymer

描述 description	ERYTHOSE-4-PHOSPHATE
分子量 formula_weight	200.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 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	432

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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	d1iria_
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	d1irib_
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	d1iric_
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	d1irid_
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	1iriA01
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	1iriA02
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	1iriA03
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	1iriB01
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	1iriB02
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	1iriB03
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	1iriC01
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	1iriC02
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	1iriC03
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	1iriD01
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	1iriD02
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	1iriD03
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	80.651 Å
晶胞边长 b length_b	107.771 Å
晶胞边长 c length_c	270.345 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	2.400 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	—
R_work r_work	0.1930
R_free r_free	0.2410

fit	/app/data/saxs_computation/ir/1iri/1iri.fit
pddf	/app/data/pr_computation/ir/1iri/1iri.pr.out
profile	/app/data/saxs_computation/ir/1iri/1iri.dat