1uc5

Structure of diol dehydratase complexed with (R)-1,2-propanediol

Method: X-RAY DIFFRACTION D_max: 122.8 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	1uc5
沉积日期 deposition_date	2003-04-08
结构标题 title	Structure of diol dehydratase complexed with (R)-1,2-propanediol
关键词 keywords	ALPHA/BETA BARREL, 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	37.18 Å
回转半径 Rg (电子) rg_electron	36.92 Å
零角强度 I(0) i0	564728000.00
分子量 molecular_weight	192400.0 kDa
排除体积 excluded_volume	239950 Å³
包络体积 envelope_volume	274250 Å³
水化壳体积 shell_volume	59972 Å³
包络直径 envelope_diameter	124.4 Å
壳层 Rg shell_rg	44.58 Å
包络 Rg envelope_rg	37.26 Å
形状 Rg shape_rg	36.93 Å
总 Rg total_rg	37.25 Å
总原子数 total_atoms	13496
残基数 n_residues	1731
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	122.8 Å
Rg (实空间) rg_real	37.21 Å
Rg 误差 (实空间) rg_real_error	0.74 Å
I(0) (实空间) i0_real	5.6470e+08
I(0) 误差 (实空间) i0_real_error	8.6570e+06
Rg (倒空间) rg_reciprocal	37.20 Å
I(0) (倒空间) i0_reciprocal	564700000.0000
解质量估计 total_estimate	0.8806
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	40.0 Å
偏度 Skewness skewness	0.374
峰度 Kurtosis kurtosis	-0.451
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	167500000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.928

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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 (8)

Entity 1 polymer

描述 description	diol dehydrase alpha subunit
分子量 formula_weight	60408.1 kDa
EC 编号 ec_number	4.2.1.28
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,L
原子数 atom_count	14220

MRSKRFEALAKRPVNQDGFVKEWIEEGFIAMESPNDPKPSIKIVNGAVTELDGKPVSDFDLIDHFIARYGINLNRAEEVMAMDSVKLANMLCDPNVKRSEIVPLTTAMTPAKIVEVVSHMNVVEMMMAMQKMRARRTPSQQAHVTNVKDNPVQIAADAAEGAWRGFDEQETTVAVARYAPFNAIALLVGSQVGRPGVLTQCSLEEATELKLGMLGHTCYAETISVYGTEPVFTDGDDTPWSKGFLASSYASRGLKMRFTSGSGSEVQMGYAEGKSMLYLEARCIYITKAAGVQGLQNGSVSCIGVPSAVPSGIRAVLAENLICSSLDLECASSNDQTFTHSDMRRTARLLMQFLPGTDFISSGYSAVPNYDNMFAGSNEDAEDFDDYNVIQRDLKVDGGLRPVREEDVIAIRNKAARALQAVFAGMGLPPITDEEVEAATYAHGSKDMPERNIVEDIKFAQEIINKNRNGLEVVKALAQGGFTDVAQDMLNIQKAKLTGDYLHTSAIIVGDGQVLSAVNDVNDYAGPATGYRLQGERWEEIKNIPGALDPNEID

来源 Source

来源生物 organism	Klebsiella oxytoca
NCBI 分类编号 ncbi_taxonomy_id	571
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	diol dehydrase beta subunit
分子量 formula_weight	24141.7 kDa
EC 编号 ec_number	4.2.1.28
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	B,E

MEINEKLLRQIIEDVLSEMKGSDKPVSFNAPAASAAPQATPPAGDGFLTEVGEARQGTQQDEVIIAVGPAFGLAQTVNIVGIPHKSILREVIAGIEEEGIKARVIRCFKSSDVAFVAVEGNRLSGSGISIGIQSKGTTVIHQQGLPPLSNLELFPQAPLLTLETYRQIGKNAARYAKRESPQPVPTLNDQMARPKYQAKSAILHIKETKYVVTGKNPQELRVAL

来源 Source

来源生物 organism	Klebsiella oxytoca
NCBI 分类编号 ncbi_taxonomy_id	571
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	diol dehydrase gamma subunit
分子量 formula_weight	19198.7 kDa
EC 编号 ec_number	4.2.1.28
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	G,M

MNTDAIESMVRDVLSRMNSLQGEAPAAAPAAGGASRSARVSDYPLANKHPEWVKTATNKTLDDFTLENVLSNKVTAQDMRITPETLRLQASIAKDAGRDRLAMNFERAAELTAVPDDRILEIYNALRPYRSTKEELLAIADDLESRYQAKICAAFVREAATLYVERKKLKGDD

来源 Source

来源生物 organism	Klebsiella oxytoca
NCBI 分类编号 ncbi_taxonomy_id	571
宿主生物 host_organism	Escherichia coli

Entity 4 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	AMMONIUM ION
分子量 formula_weight	18.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 non-polymer

描述 description	R-1,2-PROPANEDIOL
分子量 formula_weight	76.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 non-polymer

描述 description	CYANOCOBALAMIN
分子量 formula_weight	1356.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 8 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	724

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1uc5a_
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.1.19 — Cobalamin (vitamin B12)-dependent enzymes
家族 Family family	c.1.19.3 — Diol dehydratase, alpha subunit

结构域编号 domain_id	d1uc5b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.3 — B12-dependent dehydatase associated subunit
家族 Family family	c.51.3.1 — Diol dehydratase, beta subunit

结构域编号 domain_id	d1uc5e_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.3 — B12-dependent dehydatase associated subunit
家族 Family family	c.51.3.1 — Diol dehydratase, beta subunit

结构域编号 domain_id	d1uc5g_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.23 — Open three-helical up-and-down bundle
超家族 Superfamily superfamily	a.23.2 — Diol dehydratase, gamma subunit
家族 Family family	a.23.2.1 — Diol dehydratase, gamma subunit

结构域编号 domain_id	d1uc5l_
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.1.19 — Cobalamin (vitamin B12)-dependent enzymes
家族 Family family	c.1.19.3 — Diol dehydratase, alpha subunit

结构域编号 domain_id	d1uc5m_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.23 — Open three-helical up-and-down bundle
超家族 Superfamily superfamily	a.23.2 — Diol dehydratase, gamma subunit
家族 Family family	a.23.2.1 — Diol dehydratase, gamma subunit

CATH v4.4 (6 domains)

结构域编号 domain_id	1uc5A00
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	350 — Diol/glycerol dehydratase, large subunit

结构域编号 domain_id	1uc5B00
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	10150 — B12-dependent dehydatase associated subunit

结构域编号 domain_id	1uc5E00
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	10150 — B12-dependent dehydatase associated subunit

结构域编号 domain_id	1uc5G02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1510 — Hypothetical Protein Yqey; Chain: A; domain1
同源超家族 H-superfamily homologous superfamily	20 — Propanediol/glycerol dehydratase, small subunit

结构域编号 domain_id	1uc5L00
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	350 — Diol/glycerol dehydratase, large subunit

结构域编号 domain_id	1uc5M02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1510 — Hypothetical Protein Yqey; Chain: A; domain1
同源超家族 H-superfamily homologous superfamily	20 — Propanediol/glycerol dehydratase, small subunit

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7. 引用文献 (1)

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晶胞边长 a length_a	74.640 Å
晶胞边长 b length_b	122.270 Å
晶胞边长 c length_c	207.430 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	8

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	2.300 Å
最低分辨率 resolution_low	46.850 Å
R 因子 r_factor	0.2090
R_work r_work	0.2080
R_free r_free	0.2550

fit	/app/data/saxs_computation/uc/1uc5/1uc5.fit
pddf	/app/data/pr_computation/uc/1uc5/1uc5.pr.out
profile	/app/data/saxs_computation/uc/1uc5/1uc5.dat

Structure of diol dehydratase complexed with (R)-1,2-propanediol

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 (8)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)