SAXSdb — 2dw0

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2dw0
沉积日期 deposition_date	2006-08-02
结构标题 title	Crystal structure of VAP2 from Crotalus atrox venom (Form 2-1 crystal)
关键词 keywords	apoptotic toxin, SVMP, metalloproteinase, APOPTOSIS, TOXIN; APOPTOSIS, TOXIN
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	31.75 Å
回转半径 Rg (电子) rg_electron	30.98 Å
零角强度 I(0) i0	165623000.00
分子量 molecular_weight	95525.0 kDa
排除体积 excluded_volume	116540 Å³
包络体积 envelope_volume	159210 Å³
水化壳体积 shell_volume	42461 Å³
包络直径 envelope_diameter	105.9 Å
壳层 Rg shell_rg	38.54 Å
包络 Rg envelope_rg	29.95 Å
形状 Rg shape_rg	30.96 Å
总 Rg total_rg	31.70 Å
总原子数 total_atoms	6625
残基数 n_residues	828
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	100.9 Å
Rg (实空间) rg_real	31.53 Å
Rg 误差 (实空间) rg_real_error	0.92 Å
I(0) (实空间) i0_real	1.6560e+08
I(0) 误差 (实空间) i0_real_error	2.9310e+06
Rg (倒空间) rg_reciprocal	31.63 Å
I(0) (倒空间) i0_reciprocal	165600000.0000
解质量估计 total_estimate	0.8957
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	44.4 Å
偏度 Skewness skewness	0.054
峰度 Kurtosis kurtosis	-0.493
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10880000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.992

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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 (7)

Entity 1 polymer

描述 description	Catrocollastatin
分子量 formula_weight	46912.8 kDa
来源方法 src_method	nat
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	7292

HQKYNPFRFVELVLVVDKAMVTKNNGDLDKIKTRMYEIVNTVNEIYRYMYIHVALVGLEIWSNEDKITVKPEAGYTLNAFGEWRKTDLLTRKKHDNAQLLTAIDLDRVIGLAYVGSMCHPKRSTGIIQDYSEINLVVAVIMAHEMGHNLGINHDSGYCSCGDYACIMRPEISPEPSTFFSNCSYFECWDFIMNHNPECILNEPLGTDIISPPVCGNELLEVGEECDCGTPENCQNECCDAATCKLKSGSQCGHGDCCEQCKFSKSGTECRASMSECDPAEHCTGQSSECPADVFHKNGQPCLDNYGYCYNGNCPIMYHQCYDLFGADVYEAEDSCFERNQKGNYYGYCRKENGNKIPCAPEDVKCGRLYCKDNSPGQNNPCKMFYSNEDEHKGMVLPGTKCADGKVCSNGHCVDVATAY

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	951.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1114.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	6

Entity 6 non-polymer

描述 description	3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE
分子量 formula_weight	388.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 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	667

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6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id	2dw0A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	2dw0B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

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7. 引用文献 (5)

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晶胞边长 a length_a	56.910 Å
晶胞边长 b length_b	137.950 Å
晶胞边长 c length_c	59.240 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.52 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.150 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	—
R_work r_work	0.1750
R_free r_free	0.2280

fit	/app/data/saxs_computation/dw/2dw0/2dw0.fit
pddf	/app/data/pr_computation/dw/2dw0/2dw0.pr.out
profile	/app/data/saxs_computation/dw/2dw0/2dw0.dat

Crystal structure of VAP2 from Crotalus atrox venom (Form 2-1 crystal)

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