1v5b

The Structure Of The Mutant, S225A and E251L, Of 3-Isopropylmalate Dehydrogenase From Bacillus Coagulans

Method: X-RAY DIFFRACTION D_max: 214.9 Å Quality: REASONABLE

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	1v5b
沉积日期 deposition_date	2003-11-22
结构标题 title	The Structure Of The Mutant, S225A and E251L, Of 3-Isopropylmalate Dehydrogenase From Bacillus Coagulans
关键词 keywords	3-isopropylmalate dehydrogenase, IPMDH, mutant, S225A/E251L, Bacillus coagulans, homo dimer, X-ray analysis, 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	77.47 Å
回转半径 Rg (电子) rg_electron	78.37 Å
零角强度 I(0) i0	1340850000.00
分子量 molecular_weight	308980.0 kDa
排除体积 excluded_volume	387250 Å³
包络体积 envelope_volume	636800 Å³
水化壳体积 shell_volume	73488 Å³
包络直径 envelope_diameter	265.4 Å
壳层 Rg shell_rg	65.20 Å
包络 Rg envelope_rg	75.41 Å
形状 Rg shape_rg	78.37 Å
总 Rg total_rg	78.15 Å
总原子数 total_atoms	21675
残基数 n_residues	2853
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	214.9 Å
Rg (实空间) rg_real	76.38 Å
Rg 误差 (实空间) rg_real_error	1.46 Å
I(0) (实空间) i0_real	1.3270e+09
I(0) 误差 (实空间) i0_real_error	2.9600e+07
Rg (倒空间) rg_reciprocal	74.41 Å
I(0) (倒空间) i0_reciprocal	1330000000.0000
解质量估计 total_estimate	0.7441
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	43.0 Å
偏度 Skewness skewness	0.341
峰度 Kurtosis kurtosis	-0.863
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	0.0201
最高正则化参数 α highest_alpha	32840000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.522; Stabil: 0.970; Sysdev: 1.000; Positv: 1.000; Valcen: 0.673; Smooth: 0.446

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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 (3)

Entity 1 polymer

描述 description	3-isopropylmalate dehydrogenase
分子量 formula_weight	39723.4 kDa
EC 编号 ec_number	1.1.1.85
突变 mutation	S225A, E251L
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	21885

MKMKLAVLPGDGIGPEVMDAAIRVLKTVLDNDGHEAVFENALIGGAAIDEAGTPLPEETLDICRRSDAILLGAVGGPKWDHNPASLRPEKGLLGLRKEMGLFANLRPVKAYATLLNASPLKRERVENVDLVIVRELTGGLYFGRPSERRGPGENEVVDTLAYTREEIERIIEKAFQLAQIRRKKLASVDKANVLESSRMWREIAEETAKKYPDVELSHMLVDSTAMQLIANPGQFDVIVTENMFGDILSDLASVITGSLGMLPSASLRSDRFGMYEPVHGSAPDIAGQGKANPLGTVLSAALMLRYSFGLEKEAAAIEKAVDDVLQDGYCTGDLQVANGKVVSTIELTDRLIEKLNNSAAGPRIFQ

来源 Source

来源生物 organism	Bacillus coagulans
NCBI 分类编号 ncbi_taxonomy_id	1398
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

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	210

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1v5ba_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
超家族 Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
家族 Family family	c.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

结构域编号 domain_id	d1v5bb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
超家族 Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
家族 Family family	c.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

结构域编号 domain_id	d1v5bc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
超家族 Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
家族 Family family	c.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

结构域编号 domain_id	d1v5bd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
超家族 Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
家族 Family family	c.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

结构域编号 domain_id	d1v5be_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
超家族 Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
家族 Family family	c.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

结构域编号 domain_id	d1v5bf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
超家族 Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
家族 Family family	c.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

结构域编号 domain_id	d1v5bg_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
超家族 Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
家族 Family family	c.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

结构域编号 domain_id	d1v5bh_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
超家族 Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
家族 Family family	c.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

CATH v4.4 (8 domains)

结构域编号 domain_id	1v5bA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	718 — Isopropylmalate Dehydrogenase
同源超家族 H-superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

结构域编号 domain_id	1v5bB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	718 — Isopropylmalate Dehydrogenase
同源超家族 H-superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

结构域编号 domain_id	1v5bC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	718 — Isopropylmalate Dehydrogenase
同源超家族 H-superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

结构域编号 domain_id	1v5bD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	718 — Isopropylmalate Dehydrogenase
同源超家族 H-superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

结构域编号 domain_id	1v5bE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	718 — Isopropylmalate Dehydrogenase
同源超家族 H-superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

结构域编号 domain_id	1v5bF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	718 — Isopropylmalate Dehydrogenase
同源超家族 H-superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

结构域编号 domain_id	1v5bG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	718 — Isopropylmalate Dehydrogenase
同源超家族 H-superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

结构域编号 domain_id	1v5bH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	718 — Isopropylmalate Dehydrogenase
同源超家族 H-superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

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7. 引用文献 (1)

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晶胞边长 a length_a	134.200 Å
晶胞边长 b length_b	241.300 Å
晶胞边长 c length_c	114.100 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	32

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	2.950 Å
最低分辨率 resolution_low	44.450 Å
R 因子 r_factor	—
R_work r_work	0.2142
R_free r_free	0.2900

fit	/app/data/saxs_computation/v5/1v5b/1v5b.fit
pddf	/app/data/pr_computation/v5/1v5b/1v5b.pr.out
profile	/app/data/saxs_computation/v5/1v5b/1v5b.dat