1wdk

fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi, form I (native2)

Method: X-RAY DIFFRACTION D_max: 122.6 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	1wdk
沉积日期 deposition_date	2004-05-17
结构标题 title	fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi, form I (native2)
关键词 keywords	alpha2beta2 heterotetrameric complex, LYASE, OXIDOREDUCTASE-TRANSFERASE COMPLEX; LYASE,OXIDOREDUCTASE/TRANSFERASE
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	42.34 Å
回转半径 Rg (电子) rg_electron	41.87 Å
零角强度 I(0) i0	840887000.00
分子量 molecular_weight	239280.0 kDa
排除体积 excluded_volume	299640 Å³
包络体积 envelope_volume	394300 Å³
水化壳体积 shell_volume	75450 Å³
包络直径 envelope_diameter	128.3 Å
壳层 Rg shell_rg	50.31 Å
包络 Rg envelope_rg	40.47 Å
形状 Rg shape_rg	41.92 Å
总 Rg total_rg	42.08 Å
总原子数 total_atoms	16728
残基数 n_residues	2199
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	122.6 Å
Rg (实空间) rg_real	42.08 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	8.4090e+08
I(0) 误差 (实空间) i0_real_error	1.2990e+07
Rg (倒空间) rg_reciprocal	42.34 Å
I(0) (倒空间) i0_reciprocal	841100000.0000
解质量估计 total_estimate	0.8852
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	59.6 Å
偏度 Skewness skewness	-0.015
峰度 Kurtosis kurtosis	-0.670
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	92670000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.981; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.574

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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	Fatty oxidation complex alpha subunit
分子量 formula_weight	77232.3 kDa
EC 编号 ec_number	4.2.1.17, 5.3.3.8, 1.1.1.35, 5.1.2.3
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	17701

MIYEGKAITVTALESGIVELKFDLKGESVNKFNRLTLNELRQAVDAIKADASVKGVIVSSGKDVFIVGADITEFVENFKLPDAELIAGNLEANKIFSDFEDLNVPTVAAINGIALGGGLEMCLAADFRVMADSAKIGLPEVKLGIYPGFGGTVRLPRLIGVDNAVEWIASGKENRAEDALKVSAVDAVVTADKLGAAALDLIKRAISGELDYKAKRQPKLEKLKLNAIEQMMAFETAKGFVAGQAGPNYPAPVEAIKTIQKAANFGRDKALEVEAAGFAKLAKTSASNCLIGLFLNDQELKKKAKVYDKIAKDVKQAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKLLVGRVDKGRMTPAKMAEVLNGIRPTLSYGDFGNVDLVVEAVVENPKVKQAVLAEVENHVREDAILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSDLAVATTVAYAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYLMDVVGIDTGHHGRDVMAEGFPDRMKDDRRSAIDALYEAKRLGQKNGKGFYAYEADKKGKQKKLVDSSVLEVLKPIVYEQRDVTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVYGIGFPLFRGGALRYIDSIGVAEFVALADQYAELGALYHPTAKLREMAKNGQSFFG

来源 Source

来源生物 organism	Pseudomonas fragi
NCBI 分类编号 ncbi_taxonomy_id	296
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	3-ketoacyl-CoA thiolase
分子量 formula_weight	41522.7 kDa
EC 编号 ec_number	2.3.1.16
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	C,D

SLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNSKVDPGEVEDVIWGCVNQTLEQGWNIARMASLMTQIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQDAFAVRSHQLAHKATVEGKFKDEIIPMQGYDENGFLKIFDYDETIRPDTTLESLAALKPAFNPKGGTVTAGTSSQITDGASCMIVMSAQRAKDLGLEPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAGLNMADIDFIELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNGGTFGLSTMCIGLGQGIATVFERV

来源 Source

来源生物 organism	Pseudomonas fragi
NCBI 分类编号 ncbi_taxonomy_id	296
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	3,6,9,12,15-PENTAOXATRICOSAN-1-OL
分子量 formula_weight	350.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 non-polymer

描述 description	MERCURY (II) ION
分子量 formula_weight	200.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 non-polymer

描述 description	ACETYL COENZYME *A
分子量 formula_weight	809.6 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	973

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6. 折叠分类 (SCOP + CATH) 22 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1wdka1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
超家族 Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
家族 Family family	a.100.1.3 — HCDH C-domain-like

结构域编号 domain_id	d1wdka2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
超家族 Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
家族 Family family	a.100.1.3 — HCDH C-domain-like

结构域编号 domain_id	d1wdka3
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.2.1.6 — 6-phosphogluconate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1wdka4
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.3 — Crotonase-like

结构域编号 domain_id	d1wdkb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
超家族 Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
家族 Family family	a.100.1.3 — HCDH C-domain-like

结构域编号 domain_id	d1wdkb2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
超家族 Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
家族 Family family	a.100.1.3 — HCDH C-domain-like

结构域编号 domain_id	d1wdkb3
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.2.1.6 — 6-phosphogluconate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1wdkb4
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.3 — Crotonase-like

结构域编号 domain_id	d1wdkc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.95 — Thiolase-like
超家族 Superfamily superfamily	c.95.1 — Thiolase-like
家族 Family family	c.95.1.1 — Thiolase-related

结构域编号 domain_id	d1wdkc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.95 — Thiolase-like
超家族 Superfamily superfamily	c.95.1 — Thiolase-like
家族 Family family	c.95.1.1 — Thiolase-related

结构域编号 domain_id	d1wdkd1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.95 — Thiolase-like
超家族 Superfamily superfamily	c.95.1 — Thiolase-like
家族 Family family	c.95.1.1 — Thiolase-related

结构域编号 domain_id	d1wdkd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.95 — Thiolase-like
超家族 Superfamily superfamily	c.95.1 — Thiolase-like
家族 Family family	c.95.1.1 — Thiolase-related

CATH v4.4 (10 domains)

结构域编号 domain_id	1wdkA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1wdkA02
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	1wdkA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1wdkB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1wdkB02
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	1wdkB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1wdkC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

结构域编号 domain_id	1wdkC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

结构域编号 domain_id	1wdkD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

结构域编号 domain_id	1wdkD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

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7. 引用文献 (2)

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晶胞边长 a length_a	180.705 Å
晶胞边长 b length_b	94.578 Å
晶胞边长 c length_c	160.001 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	111.45 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2056
R_work r_work	0.2026
R_free r_free	0.2443

fit	/app/data/saxs_computation/wd/1wdk/1wdk.fit
pddf	/app/data/pr_computation/wd/1wdk/1wdk.pr.out
profile	/app/data/saxs_computation/wd/1wdk/1wdk.dat

fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi, form I (native2)

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 non-polymer

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) 22 domains

SCOP 2.08 (12 domains)

CATH v4.4 (10 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)