1umr

;Crystal structure of the platelet activator convulxin, a disulfide linked a4b4 cyclic tetramer from the venom of Crotalus durissus terrificus ;

Method: X-RAY DIFFRACTION D_max: 108.0 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1umr
沉积日期 deposition_date	2003-08-28
结构标题 title	;Crystal structure of the platelet activator convulxin, a disulfide linked a4b4 cyclic tetramer from the venom of Crotalus durissus terrificus ;
关键词 keywords	LECTIN, C-TYPE LECTIN, PLATELET, SUGAR-BINDING PROTEIN, ACTIVATOR, SNAKE VENOM, SUGAR BINDING PROTEIN; SUGAR 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	29.68 Å
回转半径 Rg (电子) rg_electron	29.07 Å
零角强度 I(0) i0	61830800.00
分子量 molecular_weight	61295.0 kDa
排除体积 excluded_volume	76182 Å³
包络体积 envelope_volume	95405 Å³
水化壳体积 shell_volume	28838 Å³
包络直径 envelope_diameter	112.9 Å
壳层 Rg shell_rg	34.23 Å
包络 Rg envelope_rg	29.14 Å
形状 Rg shape_rg	29.05 Å
总 Rg total_rg	29.65 Å
总原子数 total_atoms	4318
残基数 n_residues	520
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	108.0 Å
Rg (实空间) rg_real	29.80 Å
Rg 误差 (实空间) rg_real_error	1.21 Å
I(0) (实空间) i0_real	6.1830e+07
I(0) 误差 (实空间) i0_real_error	1.1290e+06
Rg (倒空间) rg_reciprocal	29.75 Å
I(0) (倒空间) i0_reciprocal	61830000.0000
解质量估计 total_estimate	0.8311
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	40.8 Å
偏度 Skewness skewness	0.443
峰度 Kurtosis kurtosis	-0.136
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	34960000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.674; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.788; 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 (3)

Entity 1 polymer

描述 description	CONVULXIN ALPHA
分子量 formula_weight	15745.9 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	4515

GLHCPSDWYYYDQHCYRIFNEEMNWEDAEWFCTKQAKGAHLVSIKSAKEADFVAWMVTQNIEESFSHVSIGLRVQNKEKQCSTKWSDGSSVSYDNLLDLYITKCSLLKKETGFRKWFVASCIGKIPFVCKFPPQC

Entity 2 polymer

描述 description	CONVULXIN BETA
分子量 formula_weight	14960.6 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	C,D

GFCCPSHWSSYDRYCYKVFKQEMTWADAEKFCTQQHTGSHLVSFHSTEEVDFVVKMTHQSLKSTFFWIGANNIWNKCNWQWSDGTKPEYKEWHEEFECLISRTFDNQWLSAPCSDTYSFVCKFEA

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	d1umra_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.1 — C-type lectin domain

结构域编号 domain_id	d1umrb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.1 — C-type lectin domain

结构域编号 domain_id	d1umrc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.1 — C-type lectin domain

结构域编号 domain_id	d1umrd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.1 — C-type lectin domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1umrA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

结构域编号 domain_id	1umrB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

结构域编号 domain_id	1umrC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

结构域编号 domain_id	1umrD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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7. 引用文献 (2)

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晶胞边长 a length_a	131.906 Å
晶胞边长 b length_b	131.906 Å
晶胞边长 c length_c	112.849 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	I 4
空间群编号 int_tables_number	79
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1900
R_work r_work	0.1870
R_free r_free	0.2640

fit	/app/data/saxs_computation/um/1umr/1umr.fit
pddf	/app/data/pr_computation/um/1umr/1umr.pr.out
profile	/app/data/saxs_computation/um/1umr/1umr.dat

;Crystal structure of the platelet activator convulxin, a disulfide linked a4b4 cyclic tetramer from the venom of Crotalus durissus terrificus ;

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

Entity 2 polymer

聚合体 Polymer

Entity 3 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)