1hwy

BOVINE GLUTAMATE DEHYDROGENASE COMPLEXED WITH NAD AND 2-OXOGLUTARATE

Method: X-RAY DIFFRACTION D_max: 142.6 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hwy
沉积日期 deposition_date	2001-01-10
结构标题 title	BOVINE GLUTAMATE DEHYDROGENASE COMPLEXED WITH NAD AND 2-OXOGLUTARATE
关键词 keywords	allostery, glutamate dehydrogenase, NAD, OXIDOREDUCTASE; 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	42.84 Å
回转半径 Rg (电子) rg_electron	42.48 Å
零角强度 I(0) i0	1841580000.00
分子量 molecular_weight	344500.0 kDa
排除体积 excluded_volume	426280 Å³
包络体积 envelope_volume	519640 Å³
水化壳体积 shell_volume	95406 Å³
包络直径 envelope_diameter	152.8 Å
壳层 Rg shell_rg	51.59 Å
包络 Rg envelope_rg	42.56 Å
形状 Rg shape_rg	42.47 Å
总 Rg total_rg	42.86 Å
总原子数 total_atoms	24168
残基数 n_residues	3006
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	142.6 Å
Rg (实空间) rg_real	42.62 Å
Rg 误差 (实空间) rg_real_error	1.01 Å
I(0) (实空间) i0_real	1.8420e+09
I(0) 误差 (实空间) i0_real_error	3.1030e+07
Rg (倒空间) rg_reciprocal	42.84 Å
I(0) (倒空间) i0_reciprocal	1842000000.0000
解质量估计 total_estimate	0.8698
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	54.0 Å
偏度 Skewness skewness	0.185
峰度 Kurtosis kurtosis	-0.341
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	520000000.0000
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: 0.780; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.990

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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 (5)

Entity 1 polymer

描述 description	GLUTAMATE DEHYDROGENASE
分子量 formula_weight	55638.2 kDa
EC 编号 ec_number	1.4.1.3
来源方法 src_method	nat
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	24468

ADREDDPNFFKMVEGFFDRGASIVEDKLVEDLKTRQTQEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSHQRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDEDLEKITRRFTMELAKKGFIGPGVDVPAPNMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFIENASYMSILGMTPGFGDKTFAVQGFGNVGLHSMRYLHRFGAKCVAVGESDGSIWNPDGIDPKELEDFKLQHGTILGFPKAKIYEGSILEVDCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPQADKIFLERNIMVIPDLYLNAGGVTVSYFQILKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFRVYNEAGVTFT

Entity 2 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	24

Entity 3 non-polymer

描述 description	2-OXOGLUTARIC ACID
分子量 formula_weight	146.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 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	12

Entity 5 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	36

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6. 折叠分类 (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1hwya1
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	d1hwya2
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	d1hwyb1
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	d1hwyb2
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	d1hwyc1
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	d1hwyc2
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	d1hwyd1
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	d1hwyd2
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	d1hwye1
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	d1hwye2
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	d1hwyf1
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	d1hwyf2
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 (18 domains)

结构域编号 domain_id	1hwyA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	140 —

结构域编号 domain_id	1hwyA02
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	1hwyA03
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	1hwyB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	140 —

结构域编号 domain_id	1hwyB02
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	1hwyB03
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	1hwyC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	140 —

结构域编号 domain_id	1hwyC02
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	1hwyC03
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	1hwyD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	140 —

结构域编号 domain_id	1hwyD02
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	1hwyD03
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	1hwyE01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	140 —

结构域编号 domain_id	1hwyE02
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	1hwyE03
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	1hwyF01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	140 —

结构域编号 domain_id	1hwyF02
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	1hwyF03
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

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7. 引用文献 (3)

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晶胞边长 a length_a	122.500 Å
晶胞边长 b length_b	101.000 Å
晶胞边长 c length_c	164.600 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	102.20 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	3.200 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	—
R_work r_work	0.2300
R_free r_free	0.2900

fit	/app/data/saxs_computation/hw/1hwy/1hwy.fit
pddf	/app/data/pr_computation/hw/1hwy/1hwy.pr.out
profile	/app/data/saxs_computation/hw/1hwy/1hwy.dat