1nr7

Crystal structure of apo bovine glutamate dehydrogenase

Method: X-RAY DIFFRACTION Dmax: 211.2 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 1nr7

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1nr7
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1. 结构基本信息 1. Structure Basics

条目编号 entry_id1nr7
沉积日期 deposition_date2003-01-23
结构标题 titleCrystal structure of apo bovine glutamate dehydrogenase
关键词 keywordsapo bovine glutamate dehydrogenase regulation allostery, OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 methodX-RAY DIFFRACTION

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

回转半径 Rg (Guinier) rg_guinier69.85
回转半径 Rg (电子) rg_electron70.38
零角强度 I(0) i06129220000.00
分子量 molecular_weight660440.0 kDa
排除体积 excluded_volume825760 ų
包络体积 envelope_volume1153800 ų
水化壳体积 shell_volume139080 ų
包络直径 envelope_diameter251.9
壳层 Rg shell_rg65.85
包络 Rg envelope_rg69.96
形状 Rg shape_rg70.37
总 Rg total_rg70.35
总原子数 total_atoms46488
残基数 n_residues5952
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

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

最大尺寸 Dmax dmax211.2
Rg (实空间) rg_real69.65
Rg 误差 (实空间) rg_real_error1.05
I(0) (实空间) i0_real6.1050e+09
I(0) 误差 (实空间) i0_real_error1.1460e+08
Rg (倒空间) rg_reciprocal68.43
I(0) (倒空间) i0_reciprocal6108000000.0000
解质量估计 total_estimate0.8067
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary57.6
偏度 Skewness skewness0.481
峰度 Kurtosis kurtosis-0.581
角度范围 angular_range— – 0.1100 −1
当前正则化参数 α current_alpha0.0379
最高正则化参数 α highest_alpha2337000000.0000
实空间数据点数 n_real_points23
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.826; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.009

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

5. 实体与聚合体信息 (1)

6. 折叠分类 (SCOP + CATH) 60 domains

SCOP 2.08 (24 domains)

结构域编号 domain_idd1nr7a1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nr7a2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nr7b1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nr7b2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nr7c1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nr7c2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nr7d1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nr7d2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nr7e1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nr7e2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nr7f1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nr7f2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nr7g1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nr7g2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nr7h1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nr7h2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nr7i1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nr7i2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nr7j1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nr7j2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nr7k1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nr7k2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nr7l1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nr7l2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases

CATH v4.4 (36 domains)

结构域编号 domain_id1nr7A01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nr7A02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nr7A03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nr7B01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nr7B02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nr7B03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nr7C01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nr7C02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nr7C03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nr7D01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nr7D02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nr7D03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nr7E01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nr7E02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nr7E03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nr7F01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nr7F02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nr7F03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nr7G01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nr7G02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nr7G03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nr7H01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nr7H02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nr7H03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nr7I01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nr7I02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nr7I03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nr7J01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nr7J02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nr7J03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nr7K01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nr7K02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nr7K03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nr7L01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nr7L02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nr7L03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140

7. 引用文献 (1)

8. 文件与曲线 (10)