SAXSdb — 1k89

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1k89
沉积日期 deposition_date	1998-06-05
结构标题 title	K89L MUTANT OF GLUTAMATE DEHYDROGENASE
关键词 keywords	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	22.87 Å
回转半径 Rg (电子) rg_electron	21.81 Å
零角强度 I(0) i0	40176400.00
分子量 molecular_weight	49106.0 kDa
排除体积 excluded_volume	61422 Å³
包络体积 envelope_volume	70843 Å³
水化壳体积 shell_volume	26527 Å³
包络直径 envelope_diameter	69.2 Å
壳层 Rg shell_rg	29.12 Å
包络 Rg envelope_rg	21.83 Å
形状 Rg shape_rg	21.82 Å
总 Rg total_rg	22.61 Å
总原子数 total_atoms	3457
残基数 n_residues	449
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	72.0 Å
Rg (实空间) rg_real	22.72 Å
Rg 误差 (实空间) rg_real_error	0.36 Å
I(0) (实空间) i0_real	4.0180e+07
I(0) 误差 (实空间) i0_real_error	4.6810e+05
Rg (倒空间) rg_reciprocal	22.75 Å
I(0) (倒空间) i0_reciprocal	40180000.0000
解质量估计 total_estimate	0.8993
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	29.9 Å
偏度 Skewness skewness	0.101
峰度 Kurtosis kurtosis	-0.519
角度范围 angular_range	— – 0.3450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10060000.0000
实空间数据点数 n_real_points	66
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.996

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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) 5 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1k89a1
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	d1k89a2
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 (3 domains)

结构域编号 domain_id	1k89A01
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	1k89A02
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	1k89A03
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 (8)

Insights into the mechanism of domain closure and substrate specificity of glutamate dehydrogenase from Clostridium symbiosum.

J.Mol.Biol. (1999)

PMID: 9878450 · DOI: 10.1006/jmbi.1998.2335 PRIMARY

Determinants of Substrate Specificity in the Superfamily of Amino Acid Dehydrogenases

Biochemistry (1997)

;The Structure of Pyrococcus Furiosus Glutamate Dehydrogenase Reveals a Key Role for Ion-Pair Networks in Maintaining Enzyme Stability at Extreme Temperatures ;

Structure (1995)

Conformational Flexibility in Glutamate Dehydrogenase. Role of Water in Substrate Recognition and Catalysis

J.Mol.Biol. (1993)

;Erratum. Structural Consequences of Sequence Patterns in the Fingerprint Region of the Nucleotide Binding Fold. Implications for Nucleotide Specificity ;

J.Mol.Biol. (1993)

;Structural Consequences of Sequence Patterns in the Fingerprint Region of the Nucleotide Binding Fold. Implications for Nucleotide Specificity ;

J.Mol.Biol. (1992)

Subunit Assembly and Active Site Location in the Structure of Glutamate Dehydrogenase

Proteins (1992)

Structural Relationship between the Hexameric and Tetrameric Family of Glutamate Dehydrogenases

Eur.J.Biochem. (1992)

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晶胞边长 a length_a	161.800 Å
晶胞边长 b length_b	161.800 Å
晶胞边长 c length_c	102.500 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	120.00 °
晶胞分子数 Z z_pdb	18

空间群 space_group	H 3 2
空间群编号 int_tables_number	155
晶系 crystal_system	—

分辨率 resolution	2.050 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

描述 description	GLUTAMATE DEHYDROGENASE
分子量 formula_weight	49199.6 kDa
EC 编号 ec_number	1.4.1.2
突变 mutation	K89L
来源方法 src_method	man
拷贝数 entity_count	1

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	3696

K89L MUTANT OF 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

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. 引用文献 (8)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Clostridium symbiosum
NCBI 分类编号 ncbi_taxonomy_id	1512
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	238

fit	/app/data/saxs_computation/k8/1k89/1k89.fit
pddf	/app/data/pr_computation/k8/1k89/1k89.pr.out
profile	/app/data/saxs_computation/k8/1k89/1k89.dat