1upt

Structure of a complex of the golgin-245 GRIP domain with Arl1

Method: X-RAY DIFFRACTION D_max: 134.8 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	1upt
沉积日期 deposition_date	2003-10-12
结构标题 title	Structure of a complex of the golgin-245 GRIP domain with Arl1
关键词 keywords	;HYDROLASE/PROTEIN-BINDING, COMPLEX (GTPASE-GOLGIN), GOLGIN-245, GRIP, ARL1, GOLGIN, GTPASE, G-PROTEIN, GOLGI, GRIP DIMER, PROTEIN SORTING, VESICLE TRAFFICKING, HYDROLASE-PROTEIN-BINDING complex ;; HYDROLASE/PROTEIN-BINDING
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	38.34 Å
回转半径 Rg (电子) rg_electron	38.39 Å
零角强度 I(0) i0	183135000.00
分子量 molecular_weight	106090.0 kDa
排除体积 excluded_volume	130920 Å³
包络体积 envelope_volume	180180 Å³
水化壳体积 shell_volume	41689 Å³
包络直径 envelope_diameter	133.7 Å
壳层 Rg shell_rg	41.04 Å
包络 Rg envelope_rg	38.29 Å
形状 Rg shape_rg	38.38 Å
总 Rg total_rg	38.61 Å
总原子数 total_atoms	7272
残基数 n_residues	845
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	134.8 Å
Rg (实空间) rg_real	38.73 Å
Rg 误差 (实空间) rg_real_error	1.49 Å
I(0) (实空间) i0_real	1.8310e+08
I(0) 误差 (实空间) i0_real_error	3.6460e+06
Rg (倒空间) rg_reciprocal	38.49 Å
I(0) (倒空间) i0_reciprocal	183100000.0000
解质量估计 total_estimate	0.7808
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	42.7 Å
偏度 Skewness skewness	0.554
峰度 Kurtosis kurtosis	-0.108
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15690000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.841; 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 (5)

Entity 1 polymer

描述 description	ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1
分子量 formula_weight	19699.6 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	A,C,E,G
原子数 atom_count	7542

GSHMTREMRILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQAMTSSEMANSLGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETLKSRQ

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 polymer

描述 description	GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4
分子量 formula_weight	7407.8 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	B,D,F,H

MGEPTEFEYLRKVLFEYMMGRETKTMAKVITTVLKFPDDQTQKILEREDARLMSWLRSSS

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 3 non-polymer

描述 description	GUANOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	523.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 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	270

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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	d1upta_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1uptb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.193 — GRIP domain
超家族 Superfamily superfamily	a.193.1 — GRIP domain
家族 Family family	a.193.1.1 — GRIP domain

结构域编号 domain_id	d1uptc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1uptd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.193 — GRIP domain
超家族 Superfamily superfamily	a.193.1 — GRIP domain
家族 Family family	a.193.1.1 — GRIP domain

结构域编号 domain_id	d1upte_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1uptf_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.193 — GRIP domain
超家族 Superfamily superfamily	a.193.1 — GRIP domain
家族 Family family	a.193.1.1 — GRIP domain

结构域编号 domain_id	d1uptg_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1upth_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.193 — GRIP domain
超家族 Superfamily superfamily	a.193.1 — GRIP domain
家族 Family family	a.193.1.1 — GRIP domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1uptA00
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	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1uptB00
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	60 — GRIP domain

结构域编号 domain_id	1uptC00
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	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1uptD00
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	60 — GRIP domain

结构域编号 domain_id	1uptE00
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	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1uptF00
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	60 — GRIP domain

结构域编号 domain_id	1uptG00
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	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1uptH00
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	60 — GRIP domain

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7. 引用文献 (1)

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晶胞边长 a length_a	72.497 Å
晶胞边长 b length_b	89.711 Å
晶胞边长 c length_c	72.534 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	110.69 °
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	1.700 Å
最低分辨率 resolution_low	67.420 Å
R 因子 r_factor	0.2220
R_work r_work	0.2210
R_free r_free	0.2520

fit	/app/data/saxs_computation/up/1upt/1upt.fit
pddf	/app/data/pr_computation/up/1upt/1upt.pr.out
profile	/app/data/saxs_computation/up/1upt/1upt.dat

Structure of a complex of the golgin-245 GRIP domain with Arl1

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

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)