SAXSdb — 2a1d

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2a1d
沉积日期 deposition_date	2005-06-20
结构标题 title	Staphylocoagulase bound to bovine thrombin
关键词 keywords	prothrombin activator, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
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	46.29 Å
回转半径 Rg (电子) rg_electron	46.50 Å
零角强度 I(0) i0	537001000.00
分子量 molecular_weight	127040.0 kDa
排除体积 excluded_volume	122820 Å³
包络体积 envelope_volume	250520 Å³
水化壳体积 shell_volume	47040 Å³
包络直径 envelope_diameter	152.5 Å
壳层 Rg shell_rg	48.62 Å
包络 Rg envelope_rg	44.66 Å
形状 Rg shape_rg	46.50 Å
总 Rg total_rg	46.56 Å
总原子数 total_atoms	9634
残基数 n_residues	1056
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	153.2 Å
Rg (实空间) rg_real	46.67 Å
Rg 误差 (实空间) rg_real_error	1.73 Å
I(0) (实空间) i0_real	5.3700e+08
I(0) 误差 (实空间) i0_real_error	9.8430e+06
Rg (倒空间) rg_reciprocal	46.30 Å
I(0) (倒空间) i0_reciprocal	536700000.0000
解质量估计 total_estimate	0.7842
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	36.0 Å
偏度 Skewness skewness	0.309
峰度 Kurtosis kurtosis	-0.982
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22830000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.540; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.699; Smooth: 0.871

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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 (6)

Entity 1 polymer

描述 description	thrombin
分子量 formula_weight	4792.3 kDa
EC 编号 ec_number	3.4.21.5
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,E
原子数 atom_count	9634

FFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR

Entity 2 polymer

描述 description	thrombin
分子量 formula_weight	29772.4 kDa
EC 编号 ec_number	3.4.21.5
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	B,F

IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDRLGS

Entity 3 polymer

描述 description	Staphylocoagulase
分子量 formula_weight	38542.0 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,H

MIVTKDYSKESRVNENSKYGTLISDWYLKGRLTSLESQFINALDILETYHYGEKEYKDAKDKLMTRILGEDQYLLERKKVQYEEYKKLYQKYKEENPTSKLKLKTFDQYTIEDLTMREYNELTESLKSAVKDFEKDVEKIENQHHDLKPFTDEMEEKATSRVDDLANKAYSVYFAFVRDTQHKTEALELKAKVDLVLGDEDKPHRISNERIEKEMIKDLESIIEDFFIETGLNKPGNITSYDSSKHHYKNHSEGFEALVKETREAVANADESWKTKTVKKYGESETKSPVVKEENKVEDPQSPKFDNQQEVKTTAGKAEETTQPVAQPL

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI 分类编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

Entity 4 non-polymer

描述 description	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
分子量 formula_weight	454.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	1

Entity 6 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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6. 折叠分类 (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

结构域编号 domain_id	2a1dA00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	140 — Epsilon-Thrombin; Chain L
同源超家族 H-superfamily homologous superfamily	10 — Thrombin light chain domain

结构域编号 domain_id	2a1dB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	10 — Trypsin-like serine proteases

结构域编号 domain_id	2a1dB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	10 — Trypsin-like serine proteases

结构域编号 domain_id	2a1dD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	750 — Staphylcoagulase, helix bundle domain 1

结构域编号 domain_id	2a1dD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	760 — Staphylcoagulase, helix bundle, domain 2

结构域编号 domain_id	2a1dE00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	140 — Epsilon-Thrombin; Chain L
同源超家族 H-superfamily homologous superfamily	10 — Thrombin light chain domain

结构域编号 domain_id	2a1dF01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	10 — Trypsin-like serine proteases

结构域编号 domain_id	2a1dF02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	10 — Trypsin-like serine proteases

结构域编号 domain_id	2a1dH01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	750 — Staphylcoagulase, helix bundle domain 1

结构域编号 domain_id	2a1dH02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	760 — Staphylcoagulase, helix bundle, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	183.780 Å
晶胞边长 b length_b	102.540 Å
晶胞边长 c length_c	134.040 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	129.14 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	3.500 Å
最低分辨率 resolution_low	31.690 Å
R 因子 r_factor	—
R_work r_work	0.2330
R_free r_free	0.3060

fit	/app/data/saxs_computation/a1/2a1d/2a1d.fit
pddf	/app/data/pr_computation/a1/2a1d/2a1d.pr.out
profile	/app/data/saxs_computation/a1/2a1d/2a1d.dat

Staphylocoagulase bound to bovine thrombin

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 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. 折叠分类 (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)