1ggt

THREE-DIMENSIONAL STRUCTURE OF A TRANSGLUTAMINASE: HUMAN BLOOD COAGULATION FACTOR XIII

Method: X-RAY DIFFRACTION D_max: 120.6 Å Quality: EXCELLENT

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ggt
沉积日期 deposition_date	1994-01-25
结构标题 title	THREE-DIMENSIONAL STRUCTURE OF A TRANSGLUTAMINASE: HUMAN BLOOD COAGULATION FACTOR XIII
关键词 keywords	BLOOD COAGULATION; BLOOD COAGULATION
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	38.89 Å
回转半径 Rg (电子) rg_electron	38.35 Å
零角强度 I(0) i0	393657000.00
分子量 molecular_weight	161470.0 kDa
排除体积 excluded_volume	201560 Å³
包络体积 envelope_volume	265310 Å³
水化壳体积 shell_volume	55853 Å³
包络直径 envelope_diameter	131.2 Å
壳层 Rg shell_rg	46.24 Å
包络 Rg envelope_rg	38.00 Å
形状 Rg shape_rg	38.34 Å
总 Rg total_rg	38.82 Å
总原子数 total_atoms	11382
残基数 n_residues	1418
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	120.6 Å
Rg (实空间) rg_real	38.73 Å
Rg 误差 (实空间) rg_real_error	0.64 Å
I(0) (实空间) i0_real	3.9370e+08
I(0) 误差 (实空间) i0_real_error	5.7610e+06
Rg (倒空间) rg_reciprocal	38.84 Å
I(0) (倒空间) i0_reciprocal	393700000.0000
解质量估计 total_estimate	0.9114
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	50.0 Å
偏度 Skewness skewness	0.140
峰度 Kurtosis kurtosis	-0.644
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	73240000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.966; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.946

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (1)

▼

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1ggta1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.9 — Transglutaminase N-terminal domain

结构域编号 domain_id	d1ggta2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.5 — Transglutaminase, two C-terminal domains
家族 Family family	b.1.5.1 — Transglutaminase, two C-terminal domains

结构域编号 domain_id	d1ggta3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.5 — Transglutaminase, two C-terminal domains
家族 Family family	b.1.5.1 — Transglutaminase, two C-terminal domains

结构域编号 domain_id	d1ggta4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.3 — Cysteine proteinases
超家族 Superfamily superfamily	d.3.1 — Cysteine proteinases
家族 Family family	d.3.1.4 — Transglutaminase core

结构域编号 domain_id	d1ggtb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.9 — Transglutaminase N-terminal domain

结构域编号 domain_id	d1ggtb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.5 — Transglutaminase, two C-terminal domains
家族 Family family	b.1.5.1 — Transglutaminase, two C-terminal domains

结构域编号 domain_id	d1ggtb3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.5 — Transglutaminase, two C-terminal domains
家族 Family family	b.1.5.1 — Transglutaminase, two C-terminal domains

结构域编号 domain_id	d1ggtb4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.3 — Cysteine proteinases
超家族 Superfamily superfamily	d.3.1 — Cysteine proteinases
家族 Family family	d.3.1.4 — Transglutaminase core

CATH v4.4 (8 domains)

结构域编号 domain_id	1ggtA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1ggtA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	260 — Coagulation Factor XIII; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Transglutaminase-like

结构域编号 domain_id	1ggtA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1ggtA04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1ggtB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1ggtB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	260 — Coagulation Factor XIII; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Transglutaminase-like

结构域编号 domain_id	1ggtB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1ggtB04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

▶

7. 引用文献 (4)

▶

晶胞边长 a length_a	101.200 Å
晶胞边长 b length_b	182.700 Å
晶胞边长 c length_c	93.400 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	8

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.650 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.2160
R_work r_work	0.2160
R_free r_free	—

描述 description	COAGULATION FACTOR XIII
分子量 formula_weight	83233.9 kDa
EC 编号 ec_number	2.3.2.13
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	11382

THREE-DIMENSIONAL STRUCTURE OF A TRANSGLUTAMINASE: HUMAN BLOOD COAGULATION FACTOR XIII

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

5. 实体与聚合体信息 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (4)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606

fit	/app/data/saxs_computation/gg/1ggt/1ggt.fit
pddf	/app/data/pr_computation/gg/1ggt/1ggt.pr.out
profile	/app/data/saxs_computation/gg/1ggt/1ggt.dat