1ovm

Crystal structure of Indolepyruvate decarboxylase from Enterobacter cloacae

Method: X-RAY DIFFRACTION D_max: 118.5 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	1ovm
沉积日期 deposition_date	2003-03-27
结构标题 title	Crystal structure of Indolepyruvate decarboxylase from Enterobacter cloacae
关键词 keywords	thiamine diphosphate, indole-3-acetic acid, indolepyruvate, tdp dependent enzyme, decarboxylase, LYASE; LYASE
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	38.21 Å
回转半径 Rg (电子) rg_electron	37.30 Å
零角强度 I(0) i0	838611000.00
分子量 molecular_weight	234880.0 kDa
排除体积 excluded_volume	292800 Å³
包络体积 envelope_volume	353240 Å³
水化壳体积 shell_volume	74382 Å³
包络直径 envelope_diameter	122.8 Å
壳层 Rg shell_rg	46.44 Å
包络 Rg envelope_rg	37.11 Å
形状 Rg shape_rg	37.29 Å
总 Rg total_rg	37.81 Å
总原子数 total_atoms	16512
残基数 n_residues	2140
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	118.5 Å
Rg (实空间) rg_real	37.94 Å
Rg 误差 (实空间) rg_real_error	0.83 Å
I(0) (实空间) i0_real	8.3860e+08
I(0) 误差 (实空间) i0_real_error	1.3380e+07
Rg (倒空间) rg_reciprocal	38.11 Å
I(0) (倒空间) i0_reciprocal	838800000.0000
解质量估计 total_estimate	0.8955
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	49.1 Å
偏度 Skewness skewness	0.118
峰度 Kurtosis kurtosis	-0.527
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	302600000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.918

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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 (4)

Entity 1 polymer

描述 description	Indole-3-pyruvate decarboxylase
分子量 formula_weight	60087.3 kDa
EC 编号 ec_number	4.1.1.74
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	16859

MRTPYCVADYLLDRLTDCGADHLFGVPGDYNLQFLDHVIDSPDICWVGCANELNASYAADGYARCKGFAALLTTFGVGELSAMNGIAGSYAEHVPVLHIVGAPGTAAQQRGELLHHTLGDGEFRHFYHMSEPITVAQAVLTEQNACYEIDRVLTTMLRERRPGYLMLPADVAKKAATPPVNALTHKQAHADSACLKAFRDAAENKLAMSKRTALLADFLVLRHGLKHALQKWVKEVPMAHATMLMGKGIFDERQAGFYGTYSGSASTGAVKEAIEGADTVLCVGTRFTDTLTAGFTHQLTPAQTIEVQPHAARVGDVWFTGIPMNQAIETLVELCKQHVHAGLMSSSSGAIPFPQPDGSLTQENFWRTLQTFIRPGDIILADQGTSAFGAIDLRLPADVNFIVQPLWGSIGYTLAAAFGAQTACPNRRVIVLTGDGAAQLTIQELGSMLRDKQHPIILVLNNEGYTVERAIHGAEQRYNDIALWNWTHIPQALSLDPQSECWRVSEAEQLADVLEKVAHHERLSLIEVMLPKADIPPLLGALTKALEACNNA

来源 Source

来源生物 organism	Enterobacter cloacae
NCBI 分类编号 ncbi_taxonomy_id	550
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	4

Entity 3 non-polymer

描述 description	THIAMINE DIPHOSPHATE
分子量 formula_weight	425.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 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	347

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1ovma1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.31 — DHS-like NAD/FAD-binding domain
超家族 Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
家族 Family family	c.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain

结构域编号 domain_id	d1ovma2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.5 — Pyruvate oxidase and decarboxylase Pyr module

结构域编号 domain_id	d1ovma3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.9 — Pyruvate oxidase and decarboxylase PP module

结构域编号 domain_id	d1ovmb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.31 — DHS-like NAD/FAD-binding domain
超家族 Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
家族 Family family	c.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain

结构域编号 domain_id	d1ovmb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.5 — Pyruvate oxidase and decarboxylase Pyr module

结构域编号 domain_id	d1ovmb3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.9 — Pyruvate oxidase and decarboxylase PP module

结构域编号 domain_id	d1ovmc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.31 — DHS-like NAD/FAD-binding domain
超家族 Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
家族 Family family	c.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain

结构域编号 domain_id	d1ovmc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.5 — Pyruvate oxidase and decarboxylase Pyr module

结构域编号 domain_id	d1ovmc3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.9 — Pyruvate oxidase and decarboxylase PP module

结构域编号 domain_id	d1ovmd1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.31 — DHS-like NAD/FAD-binding domain
超家族 Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
家族 Family family	c.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain

结构域编号 domain_id	d1ovmd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.5 — Pyruvate oxidase and decarboxylase Pyr module

结构域编号 domain_id	d1ovmd3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.9 — Pyruvate oxidase and decarboxylase PP module

CATH v4.4 (12 domains)

结构域编号 domain_id	1ovmA01
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	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	1ovmA02
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	1220 — TPP-binding domain

结构域编号 domain_id	1ovmA03
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	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	1ovmB01
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	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	1ovmB02
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	1220 — TPP-binding domain

结构域编号 domain_id	1ovmB03
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	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	1ovmC01
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	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	1ovmC02
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	1220 — TPP-binding domain

结构域编号 domain_id	1ovmC03
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	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	1ovmD01
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	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	1ovmD02
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	1220 — TPP-binding domain

结构域编号 domain_id	1ovmD03
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	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

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7. 引用文献 (1)

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晶胞边长 a length_a	132.200 Å
晶胞边长 b length_b	151.620 Å
晶胞边长 c length_c	107.550 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	16

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.650 Å
最低分辨率 resolution_low	29.560 Å
R 因子 r_factor	0.2070
R_work r_work	0.2050
R_free r_free	0.2360

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