SAXSdb — 1ycn

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ycn
沉积日期 deposition_date	2004-12-22
结构标题 title	X-RAY STRUCTURE OF ANNEXIN FROM ARABIDOPSIS THALIANA GENE AT1G35720
关键词 keywords	;STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, PSI, Center for Eukaryotic Structural GENOMICS, CESG, AT1G35720, ANNEXIN, MEMBRANE-BINDING, CALCIUM-BINDING, 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	28.68 Å
回转半径 Rg (电子) rg_electron	27.72 Å
零角强度 I(0) i0	85688600.00
分子量 molecular_weight	70614.0 kDa
排除体积 excluded_volume	87711 Å³
包络体积 envelope_volume	109720 Å³
水化壳体积 shell_volume	33004 Å³
包络直径 envelope_diameter	91.0 Å
壳层 Rg shell_rg	35.29 Å
包络 Rg envelope_rg	27.75 Å
形状 Rg shape_rg	27.72 Å
总 Rg total_rg	28.47 Å
总原子数 total_atoms	4970
残基数 n_residues	619
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	88.1 Å
Rg (实空间) rg_real	28.62 Å
Rg 误差 (实空间) rg_real_error	0.58 Å
I(0) (实空间) i0_real	8.5690e+07
I(0) 误差 (实空间) i0_real_error	1.1150e+06
Rg (倒空间) rg_reciprocal	28.64 Å
I(0) (倒空间) i0_reciprocal	85690000.0000
解质量估计 total_estimate	0.7125
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	32.0 Å
偏度 Skewness skewness	0.224
峰度 Kurtosis kurtosis	-0.576
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	24430000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 0.156; Positv: 1.000; Valcen: 0.997; Smooth: 0.894

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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 (2)

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1ycna1
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	d1ycna2
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	d1ycnb1
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	d1ycnb2
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

CATH v4.4 (8 domains)

结构域编号 domain_id	1ycnA01
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	1ycnA02
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	1ycnA03
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	1ycnA04
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	1ycnB01
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	1ycnB02
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	1ycnB03
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	1ycnB04
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	75.543 Å
晶胞边长 b length_b	96.936 Å
晶胞边长 c length_c	226.878 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	16

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.510 Å
最低分辨率 resolution_low	33.120 Å
R 因子 r_factor	0.2200
R_work r_work	0.2200
R_free r_free	0.2680

描述 description	putative Ca2+-dependent membrane-binding protein annexin
分子量 formula_weight	36212.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	5251

X-RAY STRUCTURE OF ANNEXIN FROM ARABIDOPSIS THALIANA GENE AT1G35720

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Arabidopsis thaliana
通用名 common_name	thale cress
NCBI 分类编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	281

fit	/app/data/saxs_computation/yc/1ycn/1ycn.fit
pddf	/app/data/pr_computation/yc/1ycn/1ycn.pr.out
profile	/app/data/saxs_computation/yc/1ycn/1ycn.dat