2gqd

The crystal structure of B-ketoacyl-ACP synthase II (FabF) from Staphylococcus aureus

Method: X-RAY DIFFRACTION D_max: 80.3 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	2gqd
沉积日期 deposition_date	2006-04-20
结构标题 title	The crystal structure of B-ketoacyl-ACP synthase II (FabF) from Staphylococcus aureus
关键词 keywords	duplicated BABABABB fold, TRANSFERASE; 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	26.31 Å
回转半径 Rg (电子) rg_electron	25.17 Å
零角强度 I(0) i0	127686000.00
分子量 molecular_weight	86708.0 kDa
排除体积 excluded_volume	107550 Å³
包络体积 envelope_volume	123400 Å³
水化壳体积 shell_volume	38425 Å³
包络直径 envelope_diameter	83.1 Å
壳层 Rg shell_rg	34.46 Å
包络 Rg envelope_rg	25.54 Å
形状 Rg shape_rg	25.17 Å
总 Rg total_rg	26.06 Å
总原子数 total_atoms	6085
残基数 n_residues	822
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	80.3 Å
Rg (实空间) rg_real	26.15 Å
Rg 误差 (实空间) rg_real_error	0.49 Å
I(0) (实空间) i0_real	1.2770e+08
I(0) 误差 (实空间) i0_real_error	1.9550e+06
Rg (倒空间) rg_reciprocal	26.20 Å
I(0) (倒空间) i0_reciprocal	127700000.0000
解质量估计 total_estimate	0.9025
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	77.7 Å
偏度 Skewness skewness	0.190
峰度 Kurtosis kurtosis	-0.429
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	45030000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.992

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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 (2)

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2gqda1
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	d2gqda2
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	d2gqdb1
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	d2gqdb2
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 (4 domains)

结构域编号 domain_id	2gqdA01
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	2gqdA02
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	2gqdB01
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	2gqdB02
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 (1)

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晶胞边长 a length_a	78.397 Å
晶胞边长 b length_b	78.397 Å
晶胞边长 c length_c	231.269 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 65
空间群编号 int_tables_number	170
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	29.910 Å
R 因子 r_factor	0.2235
R_work r_work	0.2209
R_free r_free	0.2732

描述 description	3-oxoacyl-[acyl-carrier-protein] synthase 2
分子量 formula_weight	46331.0 kDa
EC 编号 ec_number	2.3.1.41
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	6358

The crystal structure of B-ketoacyl-ACP synthase II (FabF) from Staphylococcus aureus

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Staphylococcus aureus
NCBI 分类编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli BL21(DE3)

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	273

fit	/app/data/saxs_computation/gq/2gqd/2gqd.fit
pddf	/app/data/pr_computation/gq/2gqd/2gqd.pr.out
profile	/app/data/saxs_computation/gq/2gqd/2gqd.dat