SAXSdb — 2d4c

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2d4c
沉积日期 deposition_date	2005-10-13
结构标题 title	Crystal structure of the endophilin BAR domain mutant
关键词 keywords	BAR domain, TRANSFERASE; TRANSFERASE
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	55.06 Å
回转半径 Rg (电子) rg_electron	56.90 Å
零角强度 I(0) i0	162665000.00
分子量 molecular_weight	102750.0 kDa
排除体积 excluded_volume	128020 Å³
包络体积 envelope_volume	184820 Å³
水化壳体积 shell_volume	33524 Å³
包络直径 envelope_diameter	232.9 Å
壳层 Rg shell_rg	44.23 Å
包络 Rg envelope_rg	58.22 Å
形状 Rg shape_rg	56.93 Å
总 Rg total_rg	56.29 Å
总原子数 total_atoms	7205
残基数 n_residues	898
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	220.8 Å
Rg (实空间) rg_real	56.47 Å
Rg 误差 (实空间) rg_real_error	4.88 Å
I(0) (实空间) i0_real	1.6270e+08
I(0) 误差 (实空间) i0_real_error	3.9240e+06
Rg (倒空间) rg_reciprocal	53.94 Å
I(0) (倒空间) i0_reciprocal	162100000.0000
解质量估计 total_estimate	0.6528
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	30.4 Å
偏度 Skewness skewness	0.797
峰度 Kurtosis kurtosis	0.123
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4956000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.195; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.105; Smooth: 0.796

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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	SH3-containing GRB2-like protein 2
分子量 formula_weight	29056.2 kDa
EC 编号 ec_number	2.3.1.-
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	7402

GPLGSMSVAGLKKQFHKATQKVSEKVGGAEGTKLDDDFKEMERKVDVTSRAVMEIMTKTIEYLQPNPASRAKLSMINTMSKIRGQEKGPGYPQAEALLAEAMLKFGRELGDDCNFGPALGEVGEAMRELSEVKDSLDIEVKQNFIDPLQNLHDKDLREIQSALQHHLKKLEGRRLDFDYKKKRQGKIPDEELRQALEKFDESKEIAESSMFNLLEMDIEQVSQLSALVQAQLEYHKQAVQILQQVTVRLEERIRQA

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	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	197

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2d4ca1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.238 — BAR/IMD domain-like
超家族 Superfamily superfamily	a.238.1 — BAR/IMD domain-like
家族 Family family	a.238.1.1 — BAR domain

结构域编号 domain_id	d2d4cb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.238 — BAR/IMD domain-like
超家族 Superfamily superfamily	a.238.1 — BAR/IMD domain-like
家族 Family family	a.238.1.1 — BAR domain

结构域编号 domain_id	d2d4cc_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.238 — BAR/IMD domain-like
超家族 Superfamily superfamily	a.238.1 — BAR/IMD domain-like
家族 Family family	a.238.1.1 — BAR domain

结构域编号 domain_id	d2d4cd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.238 — BAR/IMD domain-like
超家族 Superfamily superfamily	a.238.1 — BAR/IMD domain-like
家族 Family family	a.238.1.1 — BAR domain

CATH v4.4 (4 domains)

结构域编号 domain_id	2d4cA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
同源超家族 H-superfamily homologous superfamily	60 — Arfaptin homology (AH) domain/BAR domain

结构域编号 domain_id	2d4cB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
同源超家族 H-superfamily homologous superfamily	60 — Arfaptin homology (AH) domain/BAR domain

结构域编号 domain_id	2d4cC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
同源超家族 H-superfamily homologous superfamily	60 — Arfaptin homology (AH) domain/BAR domain

结构域编号 domain_id	2d4cD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
同源超家族 H-superfamily homologous superfamily	60 — Arfaptin homology (AH) domain/BAR domain

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7. 引用文献 (1)

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晶胞边长 a length_a	44.344 Å
晶胞边长 b length_b	212.217 Å
晶胞边长 c length_c	54.317 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.97 °
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	2.400 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2170
R_work r_work	0.2150
R_free r_free	0.2700

fit	/app/data/saxs_computation/d4/2d4c/2d4c.fit
pddf	/app/data/pr_computation/d4/2d4c/2d4c.pr.out
profile	/app/data/saxs_computation/d4/2d4c/2d4c.dat

Crystal structure of the endophilin BAR domain mutant

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