1kv3

HUMAN TISSUE TRANSGLUTAMINASE IN GDP BOUND FORM

Method: X-RAY DIFFRACTION D_max: 193.7 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	1kv3
沉积日期 deposition_date	2002-01-24
结构标题 title	HUMAN TISSUE TRANSGLUTAMINASE IN GDP BOUND FORM
关键词 keywords	tissue transglutaminase; GTP binding protein; crystallography, 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	58.31 Å
回转半径 Rg (电子) rg_electron	58.08 Å
零角强度 I(0) i0	2833130000.00
分子量 molecular_weight	441560.0 kDa
排除体积 excluded_volume	550000 Å³
包络体积 envelope_volume	802060 Å³
水化壳体积 shell_volume	113420 Å³
包络直径 envelope_diameter	196.5 Å
壳层 Rg shell_rg	61.05 Å
包络 Rg envelope_rg	57.09 Å
形状 Rg shape_rg	58.07 Å
总 Rg total_rg	58.15 Å
总原子数 total_atoms	31038
残基数 n_residues	3906
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	193.7 Å
Rg (实空间) rg_real	58.20 Å
Rg 误差 (实空间) rg_real_error	2.09 Å
I(0) (实空间) i0_real	2.8330e+09
I(0) 误差 (实空间) i0_real_error	5.7370e+07
Rg (倒空间) rg_reciprocal	58.37 Å
I(0) (倒空间) i0_reciprocal	2834000000.0000
解质量估计 total_estimate	0.8840
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	64.6 Å
偏度 Skewness skewness	0.190
峰度 Kurtosis kurtosis	-0.611
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	260400000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.757

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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-glutamine gamma-glutamyltransferase
分子量 formula_weight	77341.6 kDa
EC 编号 ec_number	2.3.2.13
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	31466

MAEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYQASVDSLTFSVVTGPAPSQEAGTKARFPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRLSLEASTGYQGSSFVLGHFILLFNAWCPADAVYLDSEEERQEYVLTQQGFIYQGSAKFIKNIPWNFGQFQDGILDICLILLDVNPKFLKNAGRDCSRRSSPVYVGRVGSGMVNCNDDQGVLLGRWDNNYGDGVSPMSWIGSVDILRRWKNHGCQRVKYGQCWVFAAVACTVLRCLGIPTRVVTNYNSAHDQNSNLLIEYFRNEFGEIQGDKSEMIWNFHCWVESWMTRPDLQPGYEGWQALDPTPQEKSEGTYCCGPVPVRAIKEGDLSTKYDAPFVFAEVNADVVDWIQQDDGSVHKSINRSLIVGLKISTKSVGRDEREDITHTYKYPEGSSEEREAFTRANHLNKLAEKEETGMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTVSYNGILGPECGTKYLLNLTLEPFSEKSVPLCILYEKYRDCLTESNLIKVRALLVEPVINSYLLAERDLYLENPEIKIRILGEPKQKRKLVAEVSLQNPLPVALEGCTFTVEGAGLTEEQKTVEIPDPVEAGEEVKVRMDLVPLHMGLHKLVVNFESDKLKAVKGFRNVIIGPA

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	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	GUANOSINE-5'-DIPHOSPHATE
分子量 formula_weight	443.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	428

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6. 折叠分类 (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

结构域编号 domain_id	d1kv3a1
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	d1kv3a2
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	d1kv3a3
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	d1kv3a4
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	d1kv3b1
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	d1kv3b2
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	d1kv3b3
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	d1kv3b4
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	d1kv3c1
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	d1kv3c2
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	d1kv3c3
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	d1kv3c4
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	d1kv3d1
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	d1kv3d2
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	d1kv3d3
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	d1kv3d4
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	d1kv3e1
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	d1kv3e2
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	d1kv3e3
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	d1kv3e4
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	d1kv3f1
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	d1kv3f2
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	d1kv3f3
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	d1kv3f4
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 (24 domains)

结构域编号 domain_id	1kv3A01
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	1kv3A02
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	1kv3A03
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	1kv3A04
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	1kv3B01
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	1kv3B02
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	1kv3B03
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	1kv3B04
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	1kv3C01
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	1kv3C02
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	1kv3C03
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	1kv3C04
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	1kv3D01
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	1kv3D02
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	1kv3D03
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	1kv3D04
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	1kv3E01
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	1kv3E02
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	1kv3E03
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	1kv3E04
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	1kv3F01
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	1kv3F02
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	1kv3F03
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	1kv3F04
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	132.479 Å
晶胞边长 b length_b	168.797 Å
晶胞边长 c length_c	238.568 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	24

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	2.800 Å
最低分辨率 resolution_low	51.790 Å
R 因子 r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.2720