2e3x

;Crystal structure of Russell's viper venom metalloproteinase ;

Method: X-RAY DIFFRACTION D_max: 128.8 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	2e3x
沉积日期 deposition_date	2006-11-30
结构标题 title	;Crystal structure of Russell's viper venom metalloproteinase ;
关键词 keywords	disintegrin, metalloproteinase, C-type lectin, HYDROLASE, BLOOD CLOTTING, TOXIN; HYDROLASE, BLOOD CLOTTING, 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	34.97 Å
回转半径 Rg (电子) rg_electron	35.42 Å
零角强度 I(0) i0	107071000.00
分子量 molecular_weight	78238.0 kDa
排除体积 excluded_volume	95966 Å³
包络体积 envelope_volume	128450 Å³
水化壳体积 shell_volume	33280 Å³
包络直径 envelope_diameter	132.1 Å
壳层 Rg shell_rg	37.43 Å
包络 Rg envelope_rg	35.72 Å
形状 Rg shape_rg	35.41 Å
总 Rg total_rg	35.60 Å
总原子数 total_atoms	5438
残基数 n_residues	665
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	128.8 Å
Rg (实空间) rg_real	35.46 Å
Rg 误差 (实空间) rg_real_error	1.95 Å
I(0) (实空间) i0_real	1.0710e+08
I(0) 误差 (实空间) i0_real_error	1.9650e+06
Rg (倒空间) rg_reciprocal	35.16 Å
I(0) (倒空间) i0_reciprocal	107000000.0000
解质量估计 total_estimate	0.7651
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	31.5 Å
偏度 Skewness skewness	0.670
峰度 Kurtosis kurtosis	-0.156
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11910000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.522; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.499; Smooth: 0.878

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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 (9)

Entity 1 polymer

描述 description	Coagulation factor X-activating enzyme heavy chain
分子量 formula_weight	47703.1 kDa
EC 编号 ec_number	3.4.24.58
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	5438

LVSTSAQFNKIFIELVIIVDHSMAKKCNSTATNTKIYEIVNSANEIFNPLNIHVTLIGVEFWCDRDLINVTSSADETLNSFGEWRASDLMTRKSHDNALLFTDMRFDLNTLGITFLAGMCQAYRSVGIVQEQGNRNFKTAVIMAHELSHNLGMYHDGKNCICNDSSCVMSPVLSDQPSKLFSNCSIHDYQRYLTRYKPKCIFNPPLRKDIVSPPVCGNEIWEEGEECDCGSPANCQNPCCDAATCKLKPGAECGNGLCCYQCKIKTAGTVCRRARDECDVPEHCTGQSAECPRDQLQQNGKPCQNNRGYCYNGDCPIMRNQCISLFGSRANVAKDSCFQENLKGSYYGYCRKENGRKIPCAPQDVKCGRLFCLNNSPRNKNPCNMHYSCMDQHKGMVDPGTKCEDGKVCNNKRQCVDVNTAYQSTTG

Entity 2 polymer

描述 description	Coagulation factor X-activating enzyme light chain 2
分子量 formula_weight	15961.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

LDCPPDSSLYRYFCYRVFKEHKTWEAAERFCMEHPNNGHLVSIESMEEAEFVAKLLSNTTGKFITHFWIGLMIKDKEQECSSEWSDGSSVSYDKLGKQEFRKCFVLEKESGYRMWFNRNCEERYLFVCKVPPEC

Entity 3 polymer

描述 description	Coagulation factor X-activating enzyme light chain 1
分子量 formula_weight	14357.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

LDCPSGWLSYEQHCYKGFNDLKNWTDAEKFCTEQKKGSHLVSLHSREEEKFVVNLISENLEYPATWIGLGNMWKDCRMEWSDRGNVKYKALAEESYCLIMITHEKVWKSMTCNFIAPVVCKF

Entity 4 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 branched

描述 description	;alpha-D-mannopyranose-(1-6)-alpha-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	748.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 7 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	1

Entity 8 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	5

Entity 9 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	1

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6. 折叠分类 (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d2e3xb_
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.169.1.0 — automated matches

结构域编号 domain_id	d2e3xc_
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.169.1.0 — automated matches

CATH v4.4 (3 domains)

结构域编号 domain_id	2e3xA01
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	2e3xB00
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	2e3xC00
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 (1)

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晶胞边长 a length_a	70.350 Å
晶胞边长 b length_b	91.730 Å
晶胞边长 c length_c	152.930 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	4

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	2.910 Å
最低分辨率 resolution_low	44.600 Å
R 因子 r_factor	—
R_work r_work	0.2180
R_free r_free	0.2730

fit	/app/data/saxs_computation/e3/2e3x/2e3x.fit
pddf	/app/data/pr_computation/e3/2e3x/2e3x.pr.out
profile	/app/data/saxs_computation/e3/2e3x/2e3x.dat

;Crystal structure of Russell's viper venom metalloproteinase ;

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 (9)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 branched

Entity 5 branched

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

6. 折叠分类 (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)