1xpk

CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS HMG-COA SYNTHASE WITH HMG-CoA AND WITH ACETOACETYL-COA AND ACETYLATED CYSTEINE

Method: X-RAY DIFFRACTION D_max: 153.4 Å Quality: REASONABLE

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1xpk
沉积日期 deposition_date	2004-10-08
结构标题 title	CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS HMG-COA SYNTHASE WITH HMG-CoA AND WITH ACETOACETYL-COA AND ACETYLATED CYSTEINE
关键词 keywords	HMG-COA Synthase, HMGS, Coenzyme A, Thiolase Fold, Condensing Enzyme, Cholesterol Biosynthesis, TRANSFERASE; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	47.54 Å
回转半径 Rg (电子) rg_electron	47.09 Å
零角强度 I(0) i0	443419000.00
分子量 molecular_weight	172450.0 kDa
排除体积 excluded_volume	213840 Å³
包络体积 envelope_volume	274710 Å³
水化壳体积 shell_volume	46431 Å³
包络直径 envelope_diameter	149.2 Å
壳层 Rg shell_rg	55.38 Å
包络 Rg envelope_rg	45.71 Å
形状 Rg shape_rg	47.10 Å
总 Rg total_rg	47.33 Å
总原子数 total_atoms	12148
残基数 n_residues	1545
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	153.4 Å
Rg (实空间) rg_real	47.78 Å
Rg 误差 (实空间) rg_real_error	1.26 Å
I(0) (实空间) i0_real	4.4340e+08
I(0) 误差 (实空间) i0_real_error	7.9540e+06
Rg (倒空间) rg_reciprocal	47.55 Å
I(0) (倒空间) i0_reciprocal	443300000.0000
解质量估计 total_estimate	0.7406
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	32.5 Å
偏度 Skewness skewness	0.183
峰度 Kurtosis kurtosis	-1.131
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	90200000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.333; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.723; Smooth: 0.901

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	3-hydroxy-3-methylglutaryl CoA synthase
分子量 formula_weight	43294.4 kDa
EC 编号 ec_number	2.3.3.10
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,D
原子数 atom_count	12897

MTIGIDKINFYVPKYYVDMAKLAEARQVDPNKFLIGIGQTEMAVSPVNQDIVSMGANAAKDIITDEDKKKIGMVIVATESAVDAAKAAAVQIHNLLGIQPFARCFEMKEACYAATPAIQLAKDYLATRPNEKVLVIATDTARYGLNSGGEPTQGAGAVAMVIAHNPSILALNEDAVAYTEDVYDFWRPTGHKYPLVDGALSKDAYIRSFQQSWNEYAKRQGKSLADFASLCFHVPFTKMGKKALESIIDNADETTQERLRSGYEDAVDYNRYVGNIYTGSLYLSLISLLENRDLQAGETIGLFSYGSGSVGEFYSATLVEGYKDHLDQAAHKALLNNRTEVSVDAYETFFKRFDDVEFDEEQDAVHEDRHIFYLSNIENNVREYHRPE

来源 Source

来源生物 organism	Staphylococcus aureus subsp. aureus
NCBI 分类编号 ncbi_taxonomy_id	46170
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	3-hydroxy-3-methylglutaryl CoA synthase
分子量 formula_weight	43252.3 kDa
EC 编号 ec_number	2.3.3.10
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

来源 Source

来源生物 organism	Staphylococcus aureus subsp. aureus
NCBI 分类编号 ncbi_taxonomy_id	46170
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 4 non-polymer

描述 description	3-HYDROXY-3-METHYLGLUTARYL-COENZYME A
分子量 formula_weight	906.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 5 non-polymer

描述 description	ACETOACETYL-COENZYME A
分子量 formula_weight	851.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	577

▼

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1xpka1
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.95.1.2 — Chalcone synthase-like

结构域编号 domain_id	d1xpka2
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.95.1.2 — Chalcone synthase-like

结构域编号 domain_id	d1xpkb1
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.95.1.2 — Chalcone synthase-like

结构域编号 domain_id	d1xpkb2
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.95.1.2 — Chalcone synthase-like

结构域编号 domain_id	d1xpkc1
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.95.1.2 — Chalcone synthase-like

结构域编号 domain_id	d1xpkc2
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.95.1.2 — Chalcone synthase-like

结构域编号 domain_id	d1xpkd1
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.95.1.2 — Chalcone synthase-like

结构域编号 domain_id	d1xpkd2
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.95.1.2 — Chalcone synthase-like

CATH v4.4 (8 domains)

结构域编号 domain_id	1xpkA01
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	1xpkA02
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	1xpkB01
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	1xpkB02
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	1xpkC01
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	1xpkC02
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	1xpkD01
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	1xpkD02
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

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	64.271 Å
晶胞边长 b length_b	84.612 Å
晶胞边长 c length_c	94.633 Å
晶胞夹角 α angle_alpha	84.25 °
晶胞夹角 β angle_beta	72.52 °
晶胞夹角 γ angle_gamma	70.44 °
晶胞分子数 Z z_pdb	3

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	35.000 Å
R 因子 r_factor	—
R_work r_work	0.1980
R_free r_free	0.2340

fit	/app/data/saxs_computation/xp/1xpk/1xpk.fit
pddf	/app/data/pr_computation/xp/1xpk/1xpk.pr.out
profile	/app/data/saxs_computation/xp/1xpk/1xpk.dat

CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS HMG-COA SYNTHASE WITH HMG-CoA AND WITH ACETOACETYL-COA AND ACETYLATED CYSTEINE

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 (6)

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 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)