SAXSdb — 1xjl

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1xjl
沉积日期 deposition_date	2004-09-23
结构标题 title	Structure of human annexin A2 in the presence of calcium ions
关键词 keywords	annexins, calcium-binding protein, lipid-binding protein, LIPID BINDING PROTEIN; LIPID 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	32.35 Å
回转半径 Rg (电子) rg_electron	32.18 Å
零角强度 I(0) i0	85399300.00
分子量 molecular_weight	73530.0 kDa
排除体积 excluded_volume	92156 Å³
包络体积 envelope_volume	119410 Å³
水化壳体积 shell_volume	32172 Å³
包络直径 envelope_diameter	110.4 Å
壳层 Rg shell_rg	37.64 Å
包络 Rg envelope_rg	31.72 Å
形状 Rg shape_rg	32.17 Å
总 Rg total_rg	32.68 Å
总原子数 total_atoms	5138
残基数 n_residues	638
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	101.9 Å
Rg (实空间) rg_real	32.52 Å
Rg 误差 (实空间) rg_real_error	0.77 Å
I(0) (实空间) i0_real	8.5400e+07
I(0) 误差 (实空间) i0_real_error	1.3140e+06
Rg (倒空间) rg_reciprocal	32.46 Å
I(0) (倒空间) i0_reciprocal	85390000.0000
解质量估计 total_estimate	0.8153
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	99.8 Å
偏度 Skewness skewness	0.367
峰度 Kurtosis kurtosis	-0.636
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13330000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.908; 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	Annexin A2
分子量 formula_weight	36536.6 kDa
突变 mutation	A66E
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,B
原子数 atom_count	5350

PSAYGSVKAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALSGHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSMKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD

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	14

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	212

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1xjla_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.65 — Annexin
超家族 Superfamily superfamily	a.65.1 — Annexin
家族 Family family	a.65.1.1 — Annexin

结构域编号 domain_id	d1xjlb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.65 — Annexin
超家族 Superfamily superfamily	a.65.1 — Annexin
家族 Family family	a.65.1.1 — Annexin

CATH v4.4 (8 domains)

结构域编号 domain_id	1xjlA01
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	10 — Annexin

结构域编号 domain_id	1xjlA02
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	10 — Annexin

结构域编号 domain_id	1xjlA03
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	10 — Annexin

结构域编号 domain_id	1xjlA04
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	10 — Annexin

结构域编号 domain_id	1xjlB01
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	10 — Annexin

结构域编号 domain_id	1xjlB02
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	10 — Annexin

结构域编号 domain_id	1xjlB03
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	10 — Annexin

结构域编号 domain_id	1xjlB04
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	10 — Annexin

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7. 引用文献 (1)

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晶胞边长 a length_a	61.781 Å
晶胞边长 b length_b	98.105 Å
晶胞边长 c length_c	176.273 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	8

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	2.590 Å
最低分辨率 resolution_low	39.060 Å
R 因子 r_factor	0.2160
R_work r_work	0.2160
R_free r_free	0.2640

fit	/app/data/saxs_computation/xj/1xjl/1xjl.fit
pddf	/app/data/pr_computation/xj/1xjl/1xjl.pr.out
profile	/app/data/saxs_computation/xj/1xjl/1xjl.dat

Structure of human annexin A2 in the presence of calcium ions

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