SAXSdb — 1hzp

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hzp
沉积日期 deposition_date	2001-01-25
结构标题 title	Crystal Structure of the Myobacterium Tuberculosis Beta-Ketoacyl-Acyl Carrier Protein Synthase III
关键词 keywords	;fatty acid biosynthesis, myobacterium tuberculosis, structural basis for substrate specificity, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC, 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	25.01 Å
回转半径 Rg (电子) rg_electron	23.86 Å
零角强度 I(0) i0	80147400.00
分子量 molecular_weight	68377.0 kDa
排除体积 excluded_volume	84834 Å³
包络体积 envelope_volume	96820 Å³
水化壳体积 shell_volume	32605 Å³
包络直径 envelope_diameter	81.0 Å
壳层 Rg shell_rg	32.32 Å
包络 Rg envelope_rg	24.10 Å
形状 Rg shape_rg	23.86 Å
总 Rg total_rg	24.69 Å
总原子数 total_atoms	4799
残基数 n_residues	654
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	79.5 Å
Rg (实空间) rg_real	24.91 Å
Rg 误差 (实空间) rg_real_error	0.46 Å
I(0) (实空间) i0_real	8.0150e+07
I(0) 误差 (实空间) i0_real_error	1.1440e+06
Rg (倒空间) rg_reciprocal	24.94 Å
I(0) (倒空间) i0_reciprocal	80150000.0000
解质量估计 total_estimate	0.8941
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	30.3 Å
偏度 Skewness skewness	0.245
峰度 Kurtosis kurtosis	-0.362
角度范围 angular_range	— – 0.3150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22850000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.978

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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 (4)

Entity 1 polymer

描述 description	3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III
分子量 formula_weight	34903.4 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 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	5057

MTEIATTSGARSVGLLSVGAYRPERVVTNDEICQHIDSSDEWIYTRTGIKTRRFAADDESAASMATEACRRALSNAGLSAADIDGVIVTTNTHFLQTPPAAPMVAASLGAKGILGFDLSAGCAGFGYALGAAADMIRGGGAATMLVVGTEKLSPTIDMYDRGNCFIFADGAAAVVVGETPFQGIGPTVAGSDGEQADAIRQDIDWITFAQNPSGPRPFVRLEGPAVFRWAAFKMGDVGRRAMDAAGVRPDQIDVFVPHQANSRINELLVKNLQLRPDAVVANDIEHTGNTSAASIPLAMAELLTTGAAKPGDLALLIGYGAGLSYAAQVVRMPKG

来源 Source

来源生物 organism	Mycobacterium tuberculosis
NCBI 分类编号 ncbi_taxonomy_id	1773
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	LAURIC ACID
分子量 formula_weight	200.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 4 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	258

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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	d1hzpa1
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	d1hzpa2
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	d1hzpb1
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	d1hzpb2
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 (4 domains)

结构域编号 domain_id	1hzpA01
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	1hzpA02
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	1hzpB01
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	1hzpB02
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	64.082 Å
晶胞边长 b length_b	54.779 Å
晶胞边长 c length_c	89.152 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.30 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.100 Å
最低分辨率 resolution_low	30.380 Å
R 因子 r_factor	0.2220
R_work r_work	0.2220
R_free r_free	0.2620

fit	/app/data/saxs_computation/hz/1hzp/1hzp.fit
pddf	/app/data/pr_computation/hz/1hzp/1hzp.pr.out
profile	/app/data/saxs_computation/hz/1hzp/1hzp.dat

Crystal Structure of the Myobacterium Tuberculosis Beta-Ketoacyl-Acyl Carrier Protein Synthase III

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