1kh3

Crystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase in complex with inhibitor

Method: X-RAY DIFFRACTION D_max: 108.1 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	1kh3
沉积日期 deposition_date	2001-11-29
结构标题 title	Crystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase in complex with inhibitor
关键词 keywords	ligase, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics; LIGASE
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	34.87 Å
回转半径 Rg (电子) rg_electron	34.01 Å
零角强度 I(0) i0	473381000.00
分子量 molecular_weight	176580.0 kDa
排除体积 excluded_volume	221010 Å³
包络体积 envelope_volume	259190 Å³
水化壳体积 shell_volume	60352 Å³
包络直径 envelope_diameter	113.5 Å
壳层 Rg shell_rg	42.82 Å
包络 Rg envelope_rg	34.14 Å
形状 Rg shape_rg	33.98 Å
总 Rg total_rg	34.67 Å
总原子数 total_atoms	12447
残基数 n_residues	1538
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	108.1 Å
Rg (实空间) rg_real	34.70 Å
Rg 误差 (实空间) rg_real_error	0.60 Å
I(0) (实空间) i0_real	4.7340e+08
I(0) 误差 (实空间) i0_real_error	7.0310e+06
Rg (倒空间) rg_reciprocal	34.80 Å
I(0) (倒空间) i0_reciprocal	473400000.0000
解质量估计 total_estimate	0.8977
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	43.3 Å
偏度 Skewness skewness	0.165
峰度 Kurtosis kurtosis	-0.489
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	120400000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.890

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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 (7)

Entity 1 polymer

描述 description	Argininosuccinate Synthetase
分子量 formula_weight	44876.0 kDa
EC 编号 ec_number	6.3.4.5
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	13014

MKIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDLKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGNDQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLLHISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDMLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYRQDLVSFDEAGGYDQKDAEGFIKIQALRLRVRALVEREGHGA

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
分子量 formula_weight	506.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 non-polymer

描述 description	ARGININE
分子量 formula_weight	175.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 non-polymer

描述 description	ASPARTIC ACID
分子量 formula_weight	133.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 7 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	567

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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	d1kh3a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
家族 Family family	c.26.2.1 — N-type ATP pyrophosphatases

结构域编号 domain_id	d1kh3a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.210 — Argininosuccinate synthetase, C-terminal domain
超家族 Superfamily superfamily	d.210.1 — Argininosuccinate synthetase, C-terminal domain
家族 Family family	d.210.1.1 — Argininosuccinate synthetase, C-terminal domain

结构域编号 domain_id	d1kh3b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
家族 Family family	c.26.2.1 — N-type ATP pyrophosphatases

结构域编号 domain_id	d1kh3b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.210 — Argininosuccinate synthetase, C-terminal domain
超家族 Superfamily superfamily	d.210.1 — Argininosuccinate synthetase, C-terminal domain
家族 Family family	d.210.1.1 — Argininosuccinate synthetase, C-terminal domain

结构域编号 domain_id	d1kh3c1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
家族 Family family	c.26.2.1 — N-type ATP pyrophosphatases

结构域编号 domain_id	d1kh3c2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.210 — Argininosuccinate synthetase, C-terminal domain
超家族 Superfamily superfamily	d.210.1 — Argininosuccinate synthetase, C-terminal domain
家族 Family family	d.210.1.1 — Argininosuccinate synthetase, C-terminal domain

结构域编号 domain_id	d1kh3d1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
家族 Family family	c.26.2.1 — N-type ATP pyrophosphatases

结构域编号 domain_id	d1kh3d2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.210 — Argininosuccinate synthetase, C-terminal domain
超家族 Superfamily superfamily	d.210.1 — Argininosuccinate synthetase, C-terminal domain
家族 Family family	d.210.1.1 — Argininosuccinate synthetase, C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1kh3A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	620 — HUPs

结构域编号 domain_id	1kh3A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1260 — Argininosuccinate synthetase, chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Argininosuccinate synthetase, chain A, domain 2

结构域编号 domain_id	1kh3B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	620 — HUPs

结构域编号 domain_id	1kh3B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1260 — Argininosuccinate synthetase, chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Argininosuccinate synthetase, chain A, domain 2

结构域编号 domain_id	1kh3C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	620 — HUPs

结构域编号 domain_id	1kh3C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1260 — Argininosuccinate synthetase, chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Argininosuccinate synthetase, chain A, domain 2

结构域编号 domain_id	1kh3D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	620 — HUPs

结构域编号 domain_id	1kh3D02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1260 — Argininosuccinate synthetase, chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Argininosuccinate synthetase, chain A, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	229.100 Å
晶胞边长 b length_b	229.100 Å
晶胞边长 c length_c	160.600 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	120.00 °
晶胞分子数 Z z_pdb	36

空间群 space_group	H 3
空间群编号 int_tables_number	146
晶系 crystal_system	—

分辨率 resolution	2.150 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	—
R_work r_work	0.2260
R_free r_free	0.2560

fit	/app/data/saxs_computation/kh/1kh3/1kh3.fit
pddf	/app/data/pr_computation/kh/1kh3/1kh3.pr.out
profile	/app/data/saxs_computation/kh/1kh3/1kh3.dat