1w96

;Crystal Structure of Biotin Carboxylase Domain of Acetyl-coenzyme A Carboxylase from Saccharomyces cerevisiae in Complex with Soraphen A ;

Method: X-RAY DIFFRACTION D_max: 128.4 Å Quality: EXCELLENT

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	1w96
沉积日期 deposition_date	2004-10-06
结构标题 title	;Crystal Structure of Biotin Carboxylase Domain of Acetyl-coenzyme A Carboxylase from Saccharomyces cerevisiae in Complex with Soraphen A ;
关键词 keywords	LIGASE, OBESITY, DIABETES, FATTY ACID METABOLISM, STRUCTURE-BASED DRUG DESIGN, ALLOSTERIC INHIBITION, POLYKETIDE; LIGASE
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	40.97 Å
回转半径 Rg (电子) rg_electron	40.41 Å
零角强度 I(0) i0	507136000.00
分子量 molecular_weight	182260.0 kDa
排除体积 excluded_volume	227260 Å³
包络体积 envelope_volume	302490 Å³
水化壳体积 shell_volume	61984 Å³
包络直径 envelope_diameter	131.9 Å
壳层 Rg shell_rg	46.26 Å
包络 Rg envelope_rg	39.60 Å
形状 Rg shape_rg	40.42 Å
总 Rg total_rg	40.69 Å
总原子数 total_atoms	12837
残基数 n_residues	1628
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	128.4 Å
Rg (实空间) rg_real	40.85 Å
Rg 误差 (实空间) rg_real_error	1.14 Å
I(0) (实空间) i0_real	5.0710e+08
I(0) 误差 (实空间) i0_real_error	8.8400e+06
Rg (倒空间) rg_reciprocal	40.97 Å
I(0) (倒空间) i0_reciprocal	507200000.0000
解质量估计 total_estimate	0.9028
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	46.1 Å
偏度 Skewness skewness	0.149
峰度 Kurtosis kurtosis	-0.642
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	50880000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.858

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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	ACETYL-COENZYME A CARBOXYLASE
分子量 formula_weight	61652.4 kDa
EC 编号 ec_number	6.4.1.2
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	14282

KMEYEITNYSERHTELPGHFIGLNTVDKLEESPLRDFVKSHGGHTVISKILIANNGIAAVKEIRSVRKWAYETFGDDRTVQFVAMATPEDLEANAEYIRMADQYIEVPGGTNNNNYANVDLIVDIAERADVDAVWAGWGHASENPLLPEKLSQSKRKVIFIGPPGNAMRSLGDKISSTIVAQSAKVPCIPWSGTGVDTVHVDEKTGLVSVDDDIYQKGCCTSPEDGLQKAKRIGFPVMIKASEGGGGKGIRQVEREEDFIALYHQAANEIPGSPIFIMKLAGRARHLEVQLLADQYGTNISLFGRDCSVQRRHQKIIEEAPVTIAKAETFHEMEKAAVRLGKLVGYVSAGTVEYLYSHDDGKFYFLELNPRLQVEHPTTEMVSGVNLPAAQLQIAMGIPMHRISDIRTLYGMNPHSASEIDFEFKTQDATKKQRRPIPKGHCTACRITSEDPNDGFKPSGGTLHELNFRSSSNVWGYFSVGNNGNIHSFSDSQFGHIFAFGENRQASRKHMVVALKELSIRGDFRTTVEYLIKLLETEDFEDNTITTGWLDDLI

来源 Source

来源生物 organism	SACCHAROMYCES CEREVISIAE
通用名 common_name	;BAKER'S YEAST ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	SORAPHEN A
分子量 formula_weight	520.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	1445

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6. 折叠分类 (SCOP + CATH) 21 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d1w96a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.84 — Barrel-sandwich hybrid
超家族 Superfamily superfamily	b.84.2 — Rudiment single hybrid motif
家族 Family family	b.84.2.1 — BC C-terminal domain-like

结构域编号 domain_id	d1w96a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.30 — PreATP-grasp domain
超家族 Superfamily superfamily	c.30.1 — PreATP-grasp domain
家族 Family family	c.30.1.1 — BC N-terminal domain-like

结构域编号 domain_id	d1w96a3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.142 — ATP-grasp
超家族 Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
家族 Family family	d.142.1.2 — BC ATP-binding domain-like

结构域编号 domain_id	d1w96b1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.84 — Barrel-sandwich hybrid
超家族 Superfamily superfamily	b.84.2 — Rudiment single hybrid motif
家族 Family family	b.84.2.1 — BC C-terminal domain-like

结构域编号 domain_id	d1w96b2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.30 — PreATP-grasp domain
超家族 Superfamily superfamily	c.30.1 — PreATP-grasp domain
家族 Family family	c.30.1.1 — BC N-terminal domain-like

结构域编号 domain_id	d1w96b3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.142 — ATP-grasp
超家族 Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
家族 Family family	d.142.1.2 — BC ATP-binding domain-like

结构域编号 domain_id	d1w96c1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.84 — Barrel-sandwich hybrid
超家族 Superfamily superfamily	b.84.2 — Rudiment single hybrid motif
家族 Family family	b.84.2.1 — BC C-terminal domain-like

结构域编号 domain_id	d1w96c2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.30 — PreATP-grasp domain
超家族 Superfamily superfamily	c.30.1 — PreATP-grasp domain
家族 Family family	c.30.1.1 — BC N-terminal domain-like

结构域编号 domain_id	d1w96c3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.142 — ATP-grasp
超家族 Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
家族 Family family	d.142.1.2 — BC ATP-binding domain-like

CATH v4.4 (12 domains)

结构域编号 domain_id	1w96A01
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	20 —

结构域编号 domain_id	1w96A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1770 — PreATP-grasp fold
同源超家族 H-superfamily homologous superfamily	10 — PreATP-grasp domain

结构域编号 domain_id	1w96A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — ATP-grasp fold, A domain

结构域编号 domain_id	1w96A04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	20 — ATP-grasp fold, B domain

结构域编号 domain_id	1w96B01
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	20 —

结构域编号 domain_id	1w96B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1770 — PreATP-grasp fold
同源超家族 H-superfamily homologous superfamily	10 — PreATP-grasp domain

结构域编号 domain_id	1w96B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — ATP-grasp fold, A domain

结构域编号 domain_id	1w96B04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	20 — ATP-grasp fold, B domain

结构域编号 domain_id	1w96C01
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	20 —

结构域编号 domain_id	1w96C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1770 — PreATP-grasp fold
同源超家族 H-superfamily homologous superfamily	10 — PreATP-grasp domain

结构域编号 domain_id	1w96C03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — ATP-grasp fold, A domain

结构域编号 domain_id	1w96C04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	20 — ATP-grasp fold, B domain

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7. 引用文献 (1)

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晶胞边长 a length_a	63.830 Å
晶胞边长 b length_b	96.520 Å
晶胞边长 c length_c	139.950 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.82 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	6

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	1.800 Å
最低分辨率 resolution_low	29.200 Å
R 因子 r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2300

fit	/app/data/saxs_computation/w9/1w96/1w96.fit
pddf	/app/data/pr_computation/w9/1w96/1w96.pr.out
profile	/app/data/saxs_computation/w9/1w96/1w96.dat