2b0o

Crystal structure of UPLC1 GAP domain

Method: X-RAY DIFFRACTION D_max: 116.3 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	2b0o
沉积日期 deposition_date	2005-09-14
结构标题 title	Crystal structure of UPLC1 GAP domain
关键词 keywords	ARFGAP, Structural Genomics, Structural Genomics Consortium, SGC, METAL BINDING PROTEIN; METAL BINDING PROTEIN
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	35.40 Å
回转半径 Rg (电子) rg_electron	34.59 Å
零角强度 I(0) i0	211197000.00
分子量 molecular_weight	114160.0 kDa
排除体积 excluded_volume	141830 Å³
包络体积 envelope_volume	179650 Å³
水化壳体积 shell_volume	43790 Å³
包络直径 envelope_diameter	119.4 Å
壳层 Rg shell_rg	40.41 Å
包络 Rg envelope_rg	34.35 Å
形状 Rg shape_rg	34.56 Å
总 Rg total_rg	35.07 Å
总原子数 total_atoms	7992
残基数 n_residues	1045
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	116.3 Å
Rg (实空间) rg_real	35.49 Å
Rg 误差 (实空间) rg_real_error	0.86 Å
I(0) (实空间) i0_real	2.1120e+08
I(0) 误差 (实空间) i0_real_error	3.5850e+06
Rg (倒空间) rg_reciprocal	35.44 Å
I(0) (倒空间) i0_reciprocal	211200000.0000
解质量估计 total_estimate	0.8758
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	38.8 Å
偏度 Skewness skewness	0.391
峰度 Kurtosis kurtosis	-0.496
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21730000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.848

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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	UPLC1
分子量 formula_weight	32785.1 kDa
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	E,F,G,H
原子数 atom_count	8492

MGSSHHHHHHSSGLVPRGSGHDGEPHDLTKLLIAEVKSRPGNSQCCDCGAADPTWLSTNLGVLTCIQCSGVHRELGVRFSRMQSLTLDLLGPSELLLALNMGNTSFNEVMEAQLPSHGGPKPSAESDMGTRRDYIMAKYVEHRFARRCTPEPQRLWTAICNRDLLSVLEAFANGQDFGQPLPGPDAQAPEELVLHLAVKVANQASLPLVDFIIQNGGHLDAKAADGNTALHYAALYNQPDCLKLLLKGRALVGTVNEAGETALDIARKKHHKECEELLEQAQAGTFAFPLHVDYSWVISTE

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 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 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	500

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2b0oe1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.45 — ArfGap/RecO-like zinc finger
超家族 Superfamily superfamily	g.45.1 — ArfGap/RecO-like zinc finger
家族 Family family	g.45.1.0 — automated matches

结构域编号 domain_id	d2b0oe2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.211 — beta-hairpin-alpha-hairpin repeat
超家族 Superfamily superfamily	d.211.1 — Ankyrin repeat
家族 Family family	d.211.1.0 — automated matches

结构域编号 domain_id	d2b0of1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.45 — ArfGap/RecO-like zinc finger
超家族 Superfamily superfamily	g.45.1 — ArfGap/RecO-like zinc finger
家族 Family family	g.45.1.0 — automated matches

结构域编号 domain_id	d2b0of2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.211 — beta-hairpin-alpha-hairpin repeat
超家族 Superfamily superfamily	d.211.1 — Ankyrin repeat
家族 Family family	d.211.1.0 — automated matches

结构域编号 domain_id	d2b0og1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.45 — ArfGap/RecO-like zinc finger
超家族 Superfamily superfamily	g.45.1 — ArfGap/RecO-like zinc finger
家族 Family family	g.45.1.0 — automated matches

结构域编号 domain_id	d2b0og2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.211 — beta-hairpin-alpha-hairpin repeat
超家族 Superfamily superfamily	d.211.1 — Ankyrin repeat
家族 Family family	d.211.1.0 — automated matches

结构域编号 domain_id	d2b0oh1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.45 — ArfGap/RecO-like zinc finger
超家族 Superfamily superfamily	g.45.1 — ArfGap/RecO-like zinc finger
家族 Family family	g.45.1.0 — automated matches

结构域编号 domain_id	d2b0oh2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.211 — beta-hairpin-alpha-hairpin repeat
超家族 Superfamily superfamily	d.211.1 — Ankyrin repeat
家族 Family family	d.211.1.0 — automated matches

CATH v4.4 (8 domains)

结构域编号 domain_id	2b0oE01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	220 — Annexin V; domain 1
同源超家族 H-superfamily homologous superfamily	150 — Arf GTPase activating protein

结构域编号 domain_id	2b0oE02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

结构域编号 domain_id	2b0oF01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	220 — Annexin V; domain 1
同源超家族 H-superfamily homologous superfamily	150 — Arf GTPase activating protein

结构域编号 domain_id	2b0oF02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

结构域编号 domain_id	2b0oG01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	220 — Annexin V; domain 1
同源超家族 H-superfamily homologous superfamily	150 — Arf GTPase activating protein

结构域编号 domain_id	2b0oG02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

结构域编号 domain_id	2b0oH01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	220 — Annexin V; domain 1
同源超家族 H-superfamily homologous superfamily	150 — Arf GTPase activating protein

结构域编号 domain_id	2b0oH02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

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7. 引用文献 (1)

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晶胞边长 a length_a	54.055 Å
晶胞边长 b length_b	106.716 Å
晶胞边长 c length_c	100.365 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.97 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.060 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.1852
R_work r_work	0.1826
R_free r_free	0.2326

fit	/app/data/saxs_computation/b0/2b0o/2b0o.fit
pddf	/app/data/pr_computation/b0/2b0o/2b0o.pr.out
profile	/app/data/saxs_computation/b0/2b0o/2b0o.dat