2glv

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) mutant(Y100A) from Helicobacter pylori

Method: X-RAY DIFFRACTION D_max: 148.0 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	2glv
沉积日期 deposition_date	2006-04-05
结构标题 title	Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) mutant(Y100A) from Helicobacter pylori
关键词 keywords	FabZ mutant, 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	43.74 Å
回转半径 Rg (电子) rg_electron	43.74 Å
零角强度 I(0) i0	541756000.00
分子量 molecular_weight	205820.0 kDa
排除体积 excluded_volume	263260 Å³
包络体积 envelope_volume	327090 Å³
水化壳体积 shell_volume	62527 Å³
包络直径 envelope_diameter	150.6 Å
壳层 Rg shell_rg	47.81 Å
包络 Rg envelope_rg	43.23 Å
形状 Rg shape_rg	43.71 Å
总 Rg total_rg	44.05 Å
总原子数 total_atoms	14527
残基数 n_residues	1813
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	148.0 Å
Rg (实空间) rg_real	43.98 Å
Rg 误差 (实空间) rg_real_error	1.31 Å
I(0) (实空间) i0_real	5.4180e+08
I(0) 误差 (实空间) i0_real_error	1.0100e+07
Rg (倒空间) rg_reciprocal	43.74 Å
I(0) (倒空间) i0_reciprocal	541600000.0000
解质量估计 total_estimate	0.7755
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	41.1 Å
偏度 Skewness skewness	0.469
峰度 Kurtosis kurtosis	-0.477
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	95780000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.717; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.925; Smooth: 0.000

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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	(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
分子量 formula_weight	19519.6 kDa
EC 编号 ec_number	4.2.1.-
突变 mutation	Y100A
来源方法 src_method	man
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	14745

MRGSHHHHHHGSMEQSHQNLQSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVAFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE

来源 Source

来源生物 organism	Helicobacter pylori
NCBI 分类编号 ncbi_taxonomy_id	102617
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

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	218

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d2glva_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
超家族 Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
家族 Family family	d.38.1.6 — FabZ-like

结构域编号 domain_id	d2glvb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
超家族 Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
家族 Family family	d.38.1.6 — FabZ-like

结构域编号 domain_id	d2glvc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
超家族 Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
家族 Family family	d.38.1.6 — FabZ-like

结构域编号 domain_id	d2glvd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
超家族 Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
家族 Family family	d.38.1.6 — FabZ-like

结构域编号 domain_id	d2glve_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
超家族 Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
家族 Family family	d.38.1.6 — FabZ-like

结构域编号 domain_id	d2glvf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
超家族 Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
家族 Family family	d.38.1.6 — FabZ-like

结构域编号 domain_id	d2glvg_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
超家族 Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
家族 Family family	d.38.1.6 — FabZ-like

结构域编号 domain_id	d2glvh_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
超家族 Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
家族 Family family	d.38.1.6 — FabZ-like

结构域编号 domain_id	d2glvi_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
超家族 Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
家族 Family family	d.38.1.6 — FabZ-like

结构域编号 domain_id	d2glvj_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
超家族 Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
家族 Family family	d.38.1.6 — FabZ-like

结构域编号 domain_id	d2glvk_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
超家族 Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
家族 Family family	d.38.1.6 — FabZ-like

结构域编号 domain_id	d2glvl_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.38 — Thioesterase/thiol ester dehydrase-isomerase
超家族 Superfamily superfamily	d.38.1 — Thioesterase/thiol ester dehydrase-isomerase
家族 Family family	d.38.1.6 — FabZ-like

CATH v4.4 (12 domains)

结构域编号 domain_id	2glvA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	129 — Thiol Ester Dehydrase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Hotdog Thioesterase

结构域编号 domain_id	2glvB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	129 — Thiol Ester Dehydrase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Hotdog Thioesterase

结构域编号 domain_id	2glvC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	129 — Thiol Ester Dehydrase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Hotdog Thioesterase

结构域编号 domain_id	2glvD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	129 — Thiol Ester Dehydrase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Hotdog Thioesterase

结构域编号 domain_id	2glvE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	129 — Thiol Ester Dehydrase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Hotdog Thioesterase

结构域编号 domain_id	2glvF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	129 — Thiol Ester Dehydrase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Hotdog Thioesterase

结构域编号 domain_id	2glvG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	129 — Thiol Ester Dehydrase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Hotdog Thioesterase

结构域编号 domain_id	2glvH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	129 — Thiol Ester Dehydrase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Hotdog Thioesterase

结构域编号 domain_id	2glvI00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	129 — Thiol Ester Dehydrase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Hotdog Thioesterase

结构域编号 domain_id	2glvJ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	129 — Thiol Ester Dehydrase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Hotdog Thioesterase

结构域编号 domain_id	2glvK00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	129 — Thiol Ester Dehydrase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Hotdog Thioesterase

结构域编号 domain_id	2glvL00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	129 — Thiol Ester Dehydrase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Hotdog Thioesterase

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7. 引用文献 (1)

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晶胞边长 a length_a	266.525 Å
晶胞边长 b length_b	76.913 Å
晶胞边长 c length_c	113.187 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	102.25 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	48

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	50.000 Å
R 因子 r_factor	—
R_work r_work	0.2400
R_free r_free	0.2930

fit	/app/data/saxs_computation/gl/2glv/2glv.fit
pddf	/app/data/pr_computation/gl/2glv/2glv.pr.out
profile	/app/data/saxs_computation/gl/2glv/2glv.dat