1ggy

HUMAN FACTOR XIII WITH YTTERBIUM BOUND IN THE ION SITE

Method: X-RAY DIFFRACTION D_max: 119.3 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	1ggy
沉积日期 deposition_date	1998-07-23
结构标题 title	HUMAN FACTOR XIII WITH YTTERBIUM BOUND IN THE ION SITE
关键词 keywords	TRANSGLUTAMINASE, BLOOD COAGULATION, YTTERBIUM, TRANSFERASE; TRANSFERASE
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	36.44 Å
回转半径 Rg (电子) rg_electron	36.15 Å
零角强度 I(0) i0	408818000.00
分子量 molecular_weight	161590.0 kDa
排除体积 excluded_volume	200410 Å³
包络体积 envelope_volume	250140 Å³
水化壳体积 shell_volume	56477 Å³
包络直径 envelope_diameter	123.2 Å
壳层 Rg shell_rg	43.17 Å
包络 Rg envelope_rg	36.40 Å
形状 Rg shape_rg	36.17 Å
总 Rg total_rg	36.52 Å
总原子数 total_atoms	11304
残基数 n_residues	1407
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	119.3 Å
Rg (实空间) rg_real	36.38 Å
Rg 误差 (实空间) rg_real_error	0.99 Å
I(0) (实空间) i0_real	4.0880e+08
I(0) 误差 (实空间) i0_real_error	6.5470e+06
Rg (倒空间) rg_reciprocal	36.42 Å
I(0) (倒空间) i0_reciprocal	408800000.0000
解质量估计 total_estimate	0.8882
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	41.6 Å
偏度 Skewness skewness	0.308
峰度 Kurtosis kurtosis	-0.380
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	76940000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.891

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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	PROTEIN (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 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	11569

SETSRTAFGGRRAVPPNNSNAAEDDLPTVELQGVVPRGVNLQEFLNVTSVHLFKERWDTNKVDHHTDKYENNKLIVRRGQSFYVQIDFSRPYDPRRDLFRVEYVIGRYPQENKGTYIPVPIVSELQSGKWGAKIVMREDRSVRLSIQSSPKCIVGKFRMYVAVWTPYGVLRTSRNPETDTYILFNPWCEDDAVYLDNEKEREEYVLNDIGVIFYGEVNDIKTRSWSYGQFEDGILDTCLYVMDRAQMDLSGRGNPIKVSRVGSAMVNAKDDEGVLVGSWDNIYAYGVPPSAWTGSVDILLEYRSSENPVRYGQCWVFAGVFNTFLRCLGIPARIVTNYFSAHDNDANLQMDIFLEEDGNVNSKLTKDSVWNYHCWNEAWMTRPDLPVGFGGWQAVDSTPQENSDGMYRCGPASVQAIKHGHVCFQFDAPFVFAEVNSDLIYITAKKDGTHVVENVDATHIGKLIVTKQIGGDGMMDITDTYKFQEGQEEERLALETALMYGAKKPLNTEGVMKSRSNVDMDFEVENAVLGKDFKLSITFRNNSHNRYTITAYLSANITFYTGVPKAEFKKETFDVTLEPLSFKKEAVLIQAGEYMGQLLEQASLHFFVTARINETRDVLAKQKSTVLTIPEIIIKVRGTQVVGSDMTVTVEFTNPLKETLRNVWVHLDGPGVTRPMKKMFREIRPNSTVQWEEVCRPWVSGHRKLIASMSSDSLRHVYGELDVQIQRRPSM

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 non-polymer

描述 description	YTTERBIUM (III) ION
分子量 formula_weight	173.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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	265

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1ggya1
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	d1ggya2
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	d1ggya3
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	d1ggya4
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	d1ggyb1
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	d1ggyb2
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	d1ggyb3
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	d1ggyb4
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	1ggyA01
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	1ggyA02
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	1ggyA03
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	1ggyA04
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	1ggyB01
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	1ggyB02
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	1ggyB03
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	1ggyB04
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

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7. 引用文献 (1)

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晶胞边长 a length_a	101.060 Å
晶胞边长 b length_b	72.390 Å
晶胞边长 c length_c	135.990 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	106.09 °
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	2.500 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.1880
R_work r_work	0.1880
R_free r_free	0.2810

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