2e9x

The crystal structure of human GINS core complex

Method: X-RAY DIFFRACTION D_max: 116.2 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2e9x
沉积日期 deposition_date	2007-01-27
结构标题 title	The crystal structure of human GINS core complex
关键词 keywords	GINS complex, Eukaryotic DNA replication, REPLICATION; REPLICATION
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	37.19 Å
回转半径 Rg (电子) rg_electron	36.48 Å
零角强度 I(0) i0	404884000.00
分子量 molecular_weight	162980.0 kDa
排除体积 excluded_volume	203840 Å³
包络体积 envelope_volume	267020 Å³
水化壳体积 shell_volume	59430 Å³
包络直径 envelope_diameter	122.0 Å
壳层 Rg shell_rg	44.15 Å
包络 Rg envelope_rg	36.08 Å
形状 Rg shape_rg	36.47 Å
总 Rg total_rg	37.00 Å
总原子数 total_atoms	11443
残基数 n_residues	1401
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	116.2 Å
Rg (实空间) rg_real	37.02 Å
Rg 误差 (实空间) rg_real_error	0.66 Å
I(0) (实空间) i0_real	4.0490e+08
I(0) 误差 (实空间) i0_real_error	6.2320e+06
Rg (倒空间) rg_reciprocal	37.13 Å
I(0) (倒空间) i0_reciprocal	404900000.0000
解质量估计 total_estimate	0.9015
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	46.0 Å
偏度 Skewness skewness	0.187
峰度 Kurtosis kurtosis	-0.493
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	62310000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.909

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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 (6)

Entity 1 polymer

描述 description	DNA replication complex GINS protein PSF1
分子量 formula_weight	17502.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,E
原子数 atom_count	11975

MFCEKAMELIRELHRAPEGQLPAFNEDGLRQVLEEMKALYEQNQSDVNEAKSGGRSDLIPTIKFRHCSLLRNRRCTVAYLYDRLLRIRALRWEYGSVLPNALRFHMAAEEMEWFNNYKRSLATYMRSLGGDEGLDITQDMKPPKSLYIE

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 polymer

描述 description	DNA replication complex GINS protein PSF2
分子量 formula_weight	21453.7 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,F

MDAAEVEFLAEKELVTIIPNFSLDKIYLIGGDLGPFNPGLPVEVPLWLAINLKQRQKCRLLPPEWMDVEKLEKMRDHERKEETFTPMPSPYYMELTKLLLNHASDNIPKADEIRTLVKDMWDTRIAKLRVSADSFVRQQEAHAKLDNLTLMEINTSGTFLTQALNHMYKLRTNLQPLESTQSQDF

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 3 polymer

描述 description	GINS complex subunit 3
分子量 formula_weight	24854.9 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,G

GPHMSEAYFRVESGALGPEENFLSLDDILMSHEKLPVRTETAMPRLGAFFLERSAGAETDNAVPQGSKLELPLWLAKGLFDNKRRILSVELPKIYQEGWRTVFSADPNVVDLHKMGPHFYGFGSQLLHFDSPENADISQSLLQTFIGRFRRIMDSSQNAYNEDTSALVARLDEMERGLFQTGQKGLNDFQCWEKGQASQITASNLVQNYKKRKFTDMED

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 4 polymer

描述 description	GINS complex subunit 4
分子量 formula_weight	26081.9 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,H

MTEEVDFLGQDSDGGSEEVVLTPAELIERLEQAWMNEKFAPELLESKPEIVECVMEQLEHMEENLRRAKREDLKVSIHQMEMERIRYVLSSYLRCRLMKIEKFFPHVLEKEKTRPEGEPSSLSPEELAFAREFMANTESYLKNVALKHMPPNLQKVDLFRAVPKPDLDSYVFLRVRERQENILVEPDTDEQRDYVIDLEKGSQHLIRYKTIAPLVASGAVQLI

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 5 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 6 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	532

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6. 折叠分类 (SCOP + CATH) 27 domains

SCOP 2.08 (15 domains)

结构域编号 domain_id	d2e9xa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.278 — GINS helical bundle-like
超家族 Superfamily superfamily	a.278.1 — GINS helical bundle-like
家族 Family family	a.278.1.1 — PSF1 N-terminal domain-like

结构域编号 domain_id	d2e9xb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.278 — GINS helical bundle-like
超家族 Superfamily superfamily	a.278.1 — GINS helical bundle-like
家族 Family family	a.278.1.2 — PSF2 C-terminal domain-like

结构域编号 domain_id	d2e9xb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.344 — GINS/PriA/YqbF domain
超家族 Superfamily superfamily	d.344.1 — PriA/YqbF domain
家族 Family family	d.344.1.0 — automated matches

结构域编号 domain_id	d2e9xc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.278 — GINS helical bundle-like
超家族 Superfamily superfamily	a.278.1 — GINS helical bundle-like
家族 Family family	a.278.1.3 — PSF3 C-terminal domain-like

结构域编号 domain_id	d2e9xc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.344 — GINS/PriA/YqbF domain
超家族 Superfamily superfamily	d.344.1 — PriA/YqbF domain
家族 Family family	d.344.1.4 — PSF3 N-terminal domain-like

结构域编号 domain_id	d2e9xc3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2e9xd1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.278 — GINS helical bundle-like
超家族 Superfamily superfamily	a.278.1 — GINS helical bundle-like
家族 Family family	a.278.1.4 — SLD5 N-terminal domain-like

结构域编号 domain_id	d2e9xd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.344 — GINS/PriA/YqbF domain
超家族 Superfamily superfamily	d.344.1 — PriA/YqbF domain
家族 Family family	d.344.1.3 — SLD5 C-terminal domain-like

结构域编号 domain_id	d2e9xe_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.278 — GINS helical bundle-like
超家族 Superfamily superfamily	a.278.1 — GINS helical bundle-like
家族 Family family	a.278.1.1 — PSF1 N-terminal domain-like

结构域编号 domain_id	d2e9xf1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.278 — GINS helical bundle-like
超家族 Superfamily superfamily	a.278.1 — GINS helical bundle-like
家族 Family family	a.278.1.2 — PSF2 C-terminal domain-like

结构域编号 domain_id	d2e9xf2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.344 — GINS/PriA/YqbF domain
超家族 Superfamily superfamily	d.344.1 — PriA/YqbF domain
家族 Family family	d.344.1.0 — automated matches

结构域编号 domain_id	d2e9xg1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.278 — GINS helical bundle-like
超家族 Superfamily superfamily	a.278.1 — GINS helical bundle-like
家族 Family family	a.278.1.3 — PSF3 C-terminal domain-like

结构域编号 domain_id	d2e9xg2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.344 — GINS/PriA/YqbF domain
超家族 Superfamily superfamily	d.344.1 — PriA/YqbF domain
家族 Family family	d.344.1.4 — PSF3 N-terminal domain-like

结构域编号 domain_id	d2e9xh1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.278 — GINS helical bundle-like
超家族 Superfamily superfamily	a.278.1 — GINS helical bundle-like
家族 Family family	a.278.1.4 — SLD5 N-terminal domain-like

结构域编号 domain_id	d2e9xh2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.344 — GINS/PriA/YqbF domain
超家族 Superfamily superfamily	d.344.1 — PriA/YqbF domain
家族 Family family	d.344.1.3 — SLD5 C-terminal domain-like

CATH v4.4 (12 domains)

结构域编号 domain_id	2e9xA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	1030 —

结构域编号 domain_id	2e9xB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	5 — Ribosomal Protein L9; domain 1
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	2e9xB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	1020 —

结构域编号 domain_id	2e9xC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	2050 —

结构域编号 domain_id	2e9xD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	1030 —

结构域编号 domain_id	2e9xD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	5 — Ribosomal Protein L9; domain 1
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	2e9xE01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	1030 —

结构域编号 domain_id	2e9xF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	5 — Ribosomal Protein L9; domain 1
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	2e9xF02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	1020 —

结构域编号 domain_id	2e9xG00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	2050 —

结构域编号 domain_id	2e9xH01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	1030 —

结构域编号 domain_id	2e9xH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	5 — Ribosomal Protein L9; domain 1
同源超家族 H-superfamily homologous superfamily	60 —

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7. 引用文献 (1)

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晶胞边长 a length_a	57.928 Å
晶胞边长 b length_b	88.741 Å
晶胞边长 c length_c	102.129 Å
晶胞夹角 α angle_alpha	104.69 °
晶胞夹角 β angle_beta	102.96 °
晶胞夹角 γ angle_gamma	95.47 °
晶胞分子数 Z z_pdb	2

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

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	29.820 Å
R 因子 r_factor	0.1990
R_work r_work	0.1970
R_free r_free	0.2330

fit	/app/data/saxs_computation/e9/2e9x/2e9x.fit
pddf	/app/data/pr_computation/e9/2e9x/2e9x.pr.out
profile	/app/data/saxs_computation/e9/2e9x/2e9x.dat

The crystal structure of human GINS core complex

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

5. 实体与聚合体信息 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 27 domains

SCOP 2.08 (15 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)