SAXSdb — 2gok

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2gok
沉积日期 deposition_date	2006-04-13
结构标题 title	Crystal structure of the imidazolonepropionase from Agrobacterium tumefaciens at 1.87 A resolution
关键词 keywords	;9252b, Imidazolonepropionase, Protein Structure Initiative II (PSI-II), Histidine metabolism, Structural Genomics, New York SGX Research Center for Structural Genomics, NYSGXRC, HYDROLASE ;; HYDROLASE
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	28.49 Å
回转半径 Rg (电子) rg_electron	27.34 Å
零角强度 I(0) i0	120605000.00
分子量 molecular_weight	86228.0 kDa
排除体积 excluded_volume	107790 Å³
包络体积 envelope_volume	125200 Å³
水化壳体积 shell_volume	37170 Å³
包络直径 envelope_diameter	91.5 Å
壳层 Rg shell_rg	35.48 Å
包络 Rg envelope_rg	27.54 Å
形状 Rg shape_rg	27.36 Å
总 Rg total_rg	28.04 Å
总原子数 total_atoms	6053
残基数 n_residues	808
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	87.0 Å
Rg (实空间) rg_real	28.34 Å
Rg 误差 (实空间) rg_real_error	0.41 Å
I(0) (实空间) i0_real	1.2060e+08
I(0) 误差 (实空间) i0_real_error	1.7040e+06
Rg (倒空间) rg_reciprocal	28.39 Å
I(0) (倒空间) i0_reciprocal	120600000.0000
解质量估计 total_estimate	0.9063
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	35.7 Å
偏度 Skewness skewness	0.184
峰度 Kurtosis kurtosis	-0.517
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	49010000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.916

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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 (6)

Entity 1 polymer

描述 description	Imidazolonepropionase
分子量 formula_weight	45660.6 kDa
EC 编号 ec_number	3.5.2.7
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	6549

MSLPGNNSAKGTATGNATALWRNAQLATLNPAMDGIGAVENAVIAVRNGRIAFAGPESDLPDDLSTADETTDCGGRWITPALIDCHTHLVFGGNRAMEFEMRLNGATYEEIAKAGGGIVSSVRDTRALSDEVLVAQALPRLDTLLSEGVSTIEIKSGYGLDIETELKMLRVARRLETLRPVRIVTSYLAAHATPADYKGRNADYITDVVLPGLEKAHAEGLADAVDGFCEGIAFSVKEIDRVFAAAQQRGLPVKLHAEQLSNLGGAELAASYNALSADHLEYLDETGAKALAKAGTVAVLLPGAFYALREKQLPPVQALRDAGAEIALATDCNPGTSPLTSLLLTMNMGATLFRMTVEECLTATTRNAAKALGLLAETGTLEAGKSADFAIWDIERPAELVYRIGFNPLHARIFKGQKVSPEGHHHHHH

来源 Source

来源生物 organism	Agrobacterium tumefaciens str.
NCBI 分类编号 ncbi_taxonomy_id	176299
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	2

Entity 4 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	1

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 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	496

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2goka1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
超家族 Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
家族 Family family	b.92.1.10 — Imidazolonepropionase-like

结构域编号 domain_id	d2goka2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
家族 Family family	c.1.9.17 — Imidazolonepropionase-like

结构域编号 domain_id	d2gokb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
超家族 Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
家族 Family family	b.92.1.10 — Imidazolonepropionase-like

结构域编号 domain_id	d2gokb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
家族 Family family	c.1.9.17 — Imidazolonepropionase-like

CATH v4.4 (4 domains)

结构域编号 domain_id	2gokA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	40 — Urease, subunit C; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Urease, subunit C, domain 1

结构域编号 domain_id	2gokA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	140 — Metal-dependent hydrolases

结构域编号 domain_id	2gokB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	40 — Urease, subunit C; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Urease, subunit C, domain 1

结构域编号 domain_id	2gokB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	140 — Metal-dependent hydrolases

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7. 引用文献 (1)

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晶胞边长 a length_a	140.754 Å
晶胞边长 b length_b	63.630 Å
晶胞边长 c length_c	103.716 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	111.93 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.870 Å
最低分辨率 resolution_low	23.640 Å
R 因子 r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2310

fit	/app/data/saxs_computation/go/2gok/2gok.fit
pddf	/app/data/pr_computation/go/2gok/2gok.pr.out
profile	/app/data/saxs_computation/go/2gok/2gok.dat

Crystal structure of the imidazolonepropionase from Agrobacterium tumefaciens at 1.87 A resolution

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution