1v9l

L-glutamate dehydrogenase from Pyrobaculum islandicum complexed with NAD

Method: X-RAY DIFFRACTION D_max: 136.6 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1v9l
沉积日期 deposition_date	2004-01-26
结构标题 title	L-glutamate dehydrogenase from Pyrobaculum islandicum complexed with NAD
关键词 keywords	Protein-NAD complex, OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	42.74 Å
回转半径 Rg (电子) rg_electron	42.15 Å
零角强度 I(0) i0	1109010000.00
分子量 molecular_weight	282930.0 kDa
排除体积 excluded_volume	357600 Å³
包络体积 envelope_volume	450830 Å³
水化壳体积 shell_volume	85891 Å³
包络直径 envelope_diameter	140.3 Å
壳层 Rg shell_rg	49.28 Å
包络 Rg envelope_rg	41.88 Å
形状 Rg shape_rg	42.12 Å
总 Rg total_rg	42.56 Å
总原子数 total_atoms	19957
残基数 n_residues	2508
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

▼

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

最大尺寸 Dmax dmax	136.6 Å
Rg (实空间) rg_real	42.55 Å
Rg 误差 (实空间) rg_real_error	1.10 Å
I(0) (实空间) i0_real	1.1090e+09
I(0) 误差 (实空间) i0_real_error	1.9070e+07
Rg (倒空间) rg_reciprocal	42.74 Å
I(0) (倒空间) i0_reciprocal	1109000000.0000
解质量估计 total_estimate	0.8829
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	55.4 Å
偏度 Skewness skewness	0.194
峰度 Kurtosis kurtosis	-0.372
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	186900000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.889

▶

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

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	glutamate dehydrogenase
分子量 formula_weight	46962.1 kDa
EC 编号 ec_number	1.4.1.2
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	20087

MERTGFLEYVLNYVKKGVELGGFPEDFYKILSRPRRVLIVNIPVRLDGGGFEVFEGYRVQHCDVLGPYKGGVRFHPEVTLADDVALAILMTLKNSLAGLPYGGAKGAVRVDPKKLSQRELEELSRGYARAIAPLIGDVVDIPAPDVGTNAQIMAWMVDEYSKIKGYNVPGVFTSKPPELWGNPVREYATGFGVAVATREMAKKLWGGIEGKTVAIQGMGNVGRWTAYWLEKMGAKVIAVSDINGVAYRKEGLNVELIQKNKGLTGPALVELFTTKDNAEFVKNPDAIFKLDVDIFVPAAIENVIRGDNAGLVKARLVVEGANGPTTPEAERILYERGVVVVPDILANAGGVIMSYLEWVENLQWYIWDEEETRKRLENIMVNNVERVYKRWQREKGWTMRDAAIVTALERIYNAMKIRGWI

来源 Source

来源生物 organism	Pyrobaculum islandicum
NCBI 分类编号 ncbi_taxonomy_id	2277
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 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	130

▼

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1v9la1
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	d1v9la2
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	d1v9lb1
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	d1v9lb2
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	d1v9lc1
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	d1v9lc2
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	d1v9ld1
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	d1v9ld2
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	d1v9le1
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	d1v9le2
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	d1v9lf1
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	d1v9lf2
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 (12 domains)

结构域编号 domain_id	1v9lA01
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	1v9lA02
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	1v9lB01
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	1v9lB02
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	1v9lC01
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	1v9lC02
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	1v9lD01
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	1v9lD02
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	1v9lE01
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	1v9lE02
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	1v9lF01
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	1v9lF02
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

▶

7. 引用文献 (2)

▶

晶胞边长 a length_a	104.210 Å
晶胞边长 b length_b	165.880 Å
晶胞边长 c length_c	181.350 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	50.000 Å
R 因子 r_factor	0.2060
R_work r_work	0.2000
R_free r_free	0.2600

fit	/app/data/saxs_computation/v9/1v9l/1v9l.fit
pddf	/app/data/pr_computation/v9/1v9l/1v9l.pr.out
profile	/app/data/saxs_computation/v9/1v9l/1v9l.dat