1nud

Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 calciums, active form)

Method: X-RAY DIFFRACTION D_max: 188.0 Å Quality: REASONABLE

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	1nud
沉积日期 deposition_date	2003-01-31
结构标题 title	Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 calciums, active form)
关键词 keywords	Transglutaminase 3, metalloenzyme, calcium ion, 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	48.92 Å
回转半径 Rg (电子) rg_electron	50.28 Å
零角强度 I(0) i0	342635000.00
分子量 molecular_weight	150380.0 kDa
排除体积 excluded_volume	187050 Å³
包络体积 envelope_volume	242750 Å³
水化壳体积 shell_volume	45046 Å³
包络直径 envelope_diameter	195.1 Å
壳层 Rg shell_rg	45.82 Å
包络 Rg envelope_rg	50.27 Å
形状 Rg shape_rg	50.28 Å
总 Rg total_rg	50.10 Å
总原子数 total_atoms	10523
残基数 n_residues	1346
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	188.0 Å
Rg (实空间) rg_real	50.06 Å
Rg 误差 (实空间) rg_real_error	2.83 Å
I(0) (实空间) i0_real	3.4260e+08
I(0) 误差 (实空间) i0_real_error	7.3660e+06
Rg (倒空间) rg_reciprocal	48.93 Å
I(0) (倒空间) i0_reciprocal	342100000.0000
解质量估计 total_estimate	0.6808
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	35.3 Å
偏度 Skewness skewness	0.634
峰度 Kurtosis kurtosis	-0.311
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	27480000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.271; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.160; Smooth: 0.872

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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 (5)

Entity 1 polymer

描述 description	Protein-glutamine glutamyltransferase E
分子量 formula_weight	76670.5 kDa
EC 编号 ec_number	2.3.2.13
突变 mutation	F264L
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	10921

AALGVQSINWQTAFNRQAHHTDKFSSQELILRRGQNFQVLMIMNKGLGSNERLEFIVSTGPYPSESAMTKAVFPLSNGSSGGWSAVLQASNGNTLTISISSPASAPIGRYTMALQIFSQGGISSVKLGTFILLFNPWLNVDSVFMGNHAEREEYVQEDAGIIFVGSTNRIGMIGWNFGQFEEDILSICLSILDRSLNFRRDAATDVASRNDPKYVGRVLSAMINSNDDNGVLAGNWSGTYTGGRDPRSWDGSVEILKNWKKSGLSPVRYGQCWVFAGTLNTALRSLGIPSRVITNFNSAHDTDRNLSVDVYYDPMGNPLDKGSDSVWNFHVWNEGWFVRSDLGPSYGGWQVLDATPQERSQGVFQCGPASVIGVREGDVQLNFDMPFIFAEVNADRITWLYDNTTGKQWKNSVNSHTIGRYISTKAVGSNARMDVTDKYKYPEGSDQERQVFQKALGKLKPNTPFAATSSMGLETEEQEPSIIGKLKVAGMLAVGKEVNLVLLLKNLSRDTKTVTVNMTAWTIIYNGTLVHEVWKDSATMSLDPEEEAEHPIKISYAQYERYLKSDNMIRITAVCKVPDESEVVVERDIILDNPTLTLEVLNEARVRKPVNVQMLFSNPLDEPVRDCVLMVEGSGLLLGNLKIDVPTLGPKERSRVRFDILPSRSGTKQLLADFSCNKFPAIKAMLSIDVAE

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	Spodoptera frugiperda

Entity 2 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	6

Entity 3 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 4 non-polymer

描述 description	BROMIDE ION
分子量 formula_weight	79.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	9

Entity 5 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	398

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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	d1nuda1
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	d1nuda2
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	d1nuda3
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	d1nuda4
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	d1nudb1
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	d1nudb2
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	d1nudb3
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	d1nudb4
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	1nudA01
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	1nudA02
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	1nudA03
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	1nudA04
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	1nudB01
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	1nudB02
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	1nudB03
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	1nudB04
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 (3)

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晶胞边长 a length_a	57.540 Å
晶胞边长 b length_b	115.370 Å
晶胞边长 c length_c	121.390 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	92.66 °
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	2.700 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.1990
R_free r_free	0.2650

fit	/app/data/saxs_computation/nu/1nud/1nud.fit
pddf	/app/data/pr_computation/nu/1nud/1nud.pr.out
profile	/app/data/saxs_computation/nu/1nud/1nud.dat