1hrd

GLUTAMATE DEHYDROGENASE

Method: X-RAY DIFFRACTION D_max: 105.2 Å Quality: EXCELLENT

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	1hrd
沉积日期 deposition_date	1996-04-03
结构标题 title	GLUTAMATE DEHYDROGENASE
关键词 keywords	OXIDOREDUCTASE, NAD; OXIDOREDUCTASE
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	35.06 Å
回转半径 Rg (电子) rg_electron	34.36 Å
零角强度 I(0) i0	331173000.00
分子量 molecular_weight	147460.0 kDa
排除体积 excluded_volume	184490 Å³
包络体积 envelope_volume	227820 Å³
水化壳体积 shell_volume	53376 Å³
包络直径 envelope_diameter	107.2 Å
壳层 Rg shell_rg	42.49 Å
包络 Rg envelope_rg	34.11 Å
形状 Rg shape_rg	34.38 Å
总 Rg total_rg	34.87 Å
总原子数 total_atoms	10380
残基数 n_residues	1347
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	105.2 Å
Rg (实空间) rg_real	34.87 Å
Rg 误差 (实空间) rg_real_error	0.53 Å
I(0) (实空间) i0_real	3.3120e+08
I(0) 误差 (实空间) i0_real_error	5.3230e+06
Rg (倒空间) rg_reciprocal	34.99 Å
I(0) (倒空间) i0_reciprocal	331200000.0000
解质量估计 total_estimate	0.9022
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	44.4 Å
偏度 Skewness skewness	0.104
峰度 Kurtosis kurtosis	-0.597
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	37660000.0000
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: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.836

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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 (2)

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6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1hrda1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

结构域编号 domain_id	d1hrda2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family family	c.58.1.1 — Aminoacid dehydrogenases

结构域编号 domain_id	d1hrdb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

结构域编号 domain_id	d1hrdb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family family	c.58.1.1 — Aminoacid dehydrogenases

结构域编号 domain_id	d1hrdc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

结构域编号 domain_id	d1hrdc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family family	c.58.1.1 — Aminoacid dehydrogenases

CATH v4.4 (9 domains)

结构域编号 domain_id	1hrdA01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1hrdA02
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	10860 — Leucine Dehydrogenase, chain A, domain 1

结构域编号 domain_id	1hrdA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	285 — Glutamate Dehydrogenase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Glutamate Dehydrogenase, chain A, domain 3

结构域编号 domain_id	1hrdB01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1hrdB02
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	10860 — Leucine Dehydrogenase, chain A, domain 1

结构域编号 domain_id	1hrdB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	285 — Glutamate Dehydrogenase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Glutamate Dehydrogenase, chain A, domain 3

结构域编号 domain_id	1hrdC01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1hrdC02
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	10860 — Leucine Dehydrogenase, chain A, domain 1

结构域编号 domain_id	1hrdC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	285 — Glutamate Dehydrogenase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Glutamate Dehydrogenase, chain A, domain 3

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7. 引用文献 (5)

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晶胞边长 a length_a	147.100 Å
晶胞边长 b length_b	151.300 Å
晶胞边长 c length_c	94.600 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	132.75 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

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	1.960 Å
最低分辨率 resolution_low	37.800 Å
R 因子 r_factor	—
R_work r_work	0.1720
R_free r_free	—

描述 description	GLUTAMATE DEHYDROGENASE
分子量 formula_weight	49215.6 kDa
EC 编号 ec_number	1.4.1.2
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	10901

GLUTAMATE DEHYDROGENASE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

Entity 2 water

6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. 引用文献 (5)

8. 文件与曲线 (10)

Files (7)

Curves (3)

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	521

fit	/app/data/saxs_computation/hr/1hrd/1hrd.fit
pddf	/app/data/pr_computation/hr/1hrd/1hrd.pr.out
profile	/app/data/saxs_computation/hr/1hrd/1hrd.dat