SAXSdb — 1ovd

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ovd
沉积日期 deposition_date	2003-03-26
结构标题 title	THE K136E MUTANT OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE A IN COMPLEX WITH OROTATE
关键词 keywords	HOMODIMER, ALPHA-BETA BARREL, FLAVOPROTEIN, OROTATE COMPLEX, MUTANT ENZYME, 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	25.95 Å
回转半径 Rg (电子) rg_electron	25.02 Å
零角强度 I(0) i0	75844300.00
分子量 molecular_weight	70132.0 kDa
排除体积 excluded_volume	88470 Å³
包络体积 envelope_volume	98788 Å³
水化壳体积 shell_volume	32290 Å³
包络直径 envelope_diameter	90.0 Å
壳层 Rg shell_rg	33.18 Å
包络 Rg envelope_rg	25.33 Å
形状 Rg shape_rg	25.01 Å
总 Rg total_rg	25.90 Å
总原子数 total_atoms	4934
残基数 n_residues	622
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	88.0 Å
Rg (实空间) rg_real	25.93 Å
Rg 误差 (实空间) rg_real_error	0.72 Å
I(0) (实空间) i0_real	7.5840e+07
I(0) 误差 (实空间) i0_real_error	1.1440e+06
Rg (倒空间) rg_reciprocal	25.94 Å
I(0) (倒空间) i0_reciprocal	75840000.0000
解质量估计 total_estimate	0.7976
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	30.3 Å
偏度 Skewness skewness	0.363
峰度 Kurtosis kurtosis	-0.315
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	34120000.0000
实空间数据点数 n_real_points	62
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.794; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.000

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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 (6)

Entity 1 polymer

描述 description	DIHYDROOROTATE DEHYDROGENASE A
分子量 formula_weight	34242.1 kDa
EC 编号 ec_number	1.3.3.1
突变 mutation	K136E
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	5427

MLNTTFANAKFANPFMNASGVHCMTIEDLEELKASQAGAYITKSSTLEKREGNPLPRYVDLELGSINSMGLPNLGFDYYLDYVLKNQKENAQEGPIFFSIAGMSAAENIAMLKKIQESDFSGITELNLSCPNVPGEPQLAYDFEATEKLLKEVFTFFTKPLGVKLPPYFDLVHFDIMAEILNQFPLTYVNSVNSIGNGLFIDPEAESVVIKPKDGFGGIGGAYIKPTALANVRAFYTRLKPEIQIIGTGGIETGQDAFEHLLCGATMLQIGTALHKEGPAIFDRIIKELEEIMNQKGYQSIADFHGKLKSL

来源 Source

来源生物 organism	Lactococcus lactis
NCBI 分类编号 ncbi_taxonomy_id	1358
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	FLAVIN MONONUCLEOTIDE
分子量 formula_weight	456.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	OROTIC ACID
分子量 formula_weight	156.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 6 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	487

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1ovda_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
家族 Family family	c.1.4.1 — FMN-linked oxidoreductases

结构域编号 domain_id	d1ovdb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
家族 Family family	c.1.4.1 — FMN-linked oxidoreductases

CATH v4.4 (4 domains)

结构域编号 domain_id	1ovdA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

结构域编号 domain_id	1ovdA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	26 — Dihydroorotate Dehydrogenase A; chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydroorotate Dehydrogenase A, chain A, domain 2

结构域编号 domain_id	1ovdB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

结构域编号 domain_id	1ovdB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	26 — Dihydroorotate Dehydrogenase A; chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydroorotate Dehydrogenase A, chain A, domain 2

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7. 引用文献 (5)

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晶胞边长 a length_a	52.870 Å
晶胞边长 b length_b	108.290 Å
晶胞边长 c length_c	65.940 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.85 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.250 Å
最低分辨率 resolution_low	12.000 Å
R 因子 r_factor	—
R_work r_work	0.1780
R_free r_free	0.2020

fit	/app/data/saxs_computation/ov/1ovd/1ovd.fit
pddf	/app/data/pr_computation/ov/1ovd/1ovd.pr.out
profile	/app/data/saxs_computation/ov/1ovd/1ovd.dat

THE K136E MUTANT OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE A IN COMPLEX WITH OROTATE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution