SAXSdb — 1vdf

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1vdf
沉积日期 deposition_date	1996-09-12
结构标题 title	ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN
关键词 keywords	EXTRACELLULAR MATRIX PROTEIN, ASSEMBLY DOMAIN, CARTILAGE, OLIGOMERIC MATRIX PROTEIN, GLYCOPROTEIN; EXTRACELLULAR MATRIX 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	22.03 Å
回转半径 Rg (电子) rg_electron	21.17 Å
零角强度 I(0) i0	13810900.00
分子量 molecular_weight	26491.0 kDa
排除体积 excluded_volume	32687 Å³
包络体积 envelope_volume	39255 Å³
水化壳体积 shell_volume	16975 Å³
包络直径 envelope_diameter	77.4 Å
壳层 Rg shell_rg	26.53 Å
包络 Rg envelope_rg	21.73 Å
形状 Rg shape_rg	21.05 Å
总 Rg total_rg	22.29 Å
总原子数 total_atoms	1831
残基数 n_residues	230
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	76.6 Å
Rg (实空间) rg_real	22.33 Å
Rg 误差 (实空间) rg_real_error	0.62 Å
I(0) (实空间) i0_real	1.3810e+07
I(0) 误差 (实空间) i0_real_error	2.0850e+05
Rg (倒空间) rg_reciprocal	22.28 Å
I(0) (倒空间) i0_reciprocal	13810000.0000
解质量估计 total_estimate	0.7783
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	20.6 Å
偏度 Skewness skewness	0.629
峰度 Kurtosis kurtosis	-0.157
角度范围 angular_range	— – 0.3600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7458000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.512; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.635; Smooth: 0.942

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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	CARTILAGE OLIGOMERIC MATRIX PROTEIN
分子量 formula_weight	5299.1 kDa
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E
原子数 atom_count	2000

MDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDACG

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 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	169

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1vdfa_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.7 — Assembly domain of cartilage oligomeric matrix protein
家族 Family family	h.1.7.1 — Assembly domain of cartilage oligomeric matrix protein

结构域编号 domain_id	d1vdfb_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.7 — Assembly domain of cartilage oligomeric matrix protein
家族 Family family	h.1.7.1 — Assembly domain of cartilage oligomeric matrix protein

结构域编号 domain_id	d1vdfc_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.7 — Assembly domain of cartilage oligomeric matrix protein
家族 Family family	h.1.7.1 — Assembly domain of cartilage oligomeric matrix protein

结构域编号 domain_id	d1vdfd_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.7 — Assembly domain of cartilage oligomeric matrix protein
家族 Family family	h.1.7.1 — Assembly domain of cartilage oligomeric matrix protein

结构域编号 domain_id	d1vdfe_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.7 — Assembly domain of cartilage oligomeric matrix protein
家族 Family family	h.1.7.1 — Assembly domain of cartilage oligomeric matrix protein

CATH v4.4 (5 domains)

结构域编号 domain_id	1vdfA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1vdfB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1vdfC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1vdfD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1vdfE00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (2)

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晶胞边长 a length_a	38.470 Å
晶胞边长 b length_b	49.470 Å
晶胞边长 c length_c	54.980 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.84 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	10

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	2.050 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	—
R_work r_work	0.1760
R_free r_free	—

fit	/app/data/saxs_computation/vd/1vdf/1vdf.fit
pddf	/app/data/pr_computation/vd/1vdf/1vdf.pr.out
profile	/app/data/saxs_computation/vd/1vdf/1vdf.dat

ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 water

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)