SAXSdb — 1hkv

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hkv
沉积日期 deposition_date	2003-03-11
结构标题 title	mycobacterium diaminopimelate dicarboxylase (lysa)
关键词 keywords	;LYASE, DECARBOXYLASE, DIAMINOPIMELATE, DAPDC, PLP, LYSINE PATHWAY, MYCBACTERIUM TUBERCULOSIS, LYSINE SYNTHETIC PATHWAY, PYRIDOXAL PHOSPHATE, PSI, PROTEIN STRUCTURE INITIATIVE, TB STRUCTURAL GENOMICS CONSORTIUM, TB, TBSGC ;; 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	29.00 Å
回转半径 Rg (电子) rg_electron	28.16 Å
零角强度 I(0) i0	147993000.00
分子量 molecular_weight	95338.0 kDa
排除体积 excluded_volume	118930 Å³
包络体积 envelope_volume	139810 Å³
水化壳体积 shell_volume	40191 Å³
包络直径 envelope_diameter	102.6 Å
壳层 Rg shell_rg	36.46 Å
包络 Rg envelope_rg	28.19 Å
形状 Rg shape_rg	28.16 Å
总 Rg total_rg	28.87 Å
总原子数 total_atoms	6710
残基数 n_residues	892
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	94.2 Å
Rg (实空间) rg_real	28.91 Å
Rg 误差 (实空间) rg_real_error	0.46 Å
I(0) (实空间) i0_real	1.4800e+08
I(0) 误差 (实空间) i0_real_error	2.0710e+06
Rg (倒空间) rg_reciprocal	28.95 Å
I(0) (倒空间) i0_reciprocal	148000000.0000
解质量估计 total_estimate	0.6747
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	34.3 Å
偏度 Skewness skewness	0.279
峰度 Kurtosis kurtosis	-0.345
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	69060000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.999; Smooth: 0.962

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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	DIAMINOPIMELATE DECARBOXYLASE
分子量 formula_weight	48339.6 kDa
EC 编号 ec_number	4.1.1.20
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	6946

MNELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVDVSATAHRRYVSVDGGMSDNIRTALYGAQYDVRLVSRVSDAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSLEVRHHHHHH

来源 Source

来源生物 organism	MYCOBACTERIUM TUBERCULOSIS
NCBI 分类编号 ncbi_taxonomy_id	83332
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	LYSINE
分子量 formula_weight	147.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	PYRIDOXAL-5'-PHOSPHATE
分子量 formula_weight	247.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	236

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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	d1hkva1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamily	b.49.2 — Alanine racemase C-terminal domain-like
家族 Family family	b.49.2.3 — Eukaryotic ODC-like

结构域编号 domain_id	d1hkva2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.6 — PLP-binding barrel
家族 Family family	c.1.6.1 — Alanine racemase-like, N-terminal domain

结构域编号 domain_id	d1hkvb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamily	b.49.2 — Alanine racemase C-terminal domain-like
家族 Family family	b.49.2.3 — Eukaryotic ODC-like

结构域编号 domain_id	d1hkvb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.6 — PLP-binding barrel
家族 Family family	c.1.6.1 — Alanine racemase-like, N-terminal domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1hkvA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	37 — Lyase, Ornithine Decarboxylase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Lyase, Ornithine Decarboxylase; Chain A, domain 1

结构域编号 domain_id	1hkvA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	10 — Alanine racemase

结构域编号 domain_id	1hkvB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	37 — Lyase, Ornithine Decarboxylase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Lyase, Ornithine Decarboxylase; Chain A, domain 1

结构域编号 domain_id	1hkvB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	10 — Alanine racemase

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7. 引用文献 (1)

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晶胞边长 a length_a	111.452 Å
晶胞边长 b length_b	111.452 Å
晶胞边长 c length_c	238.253 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	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	18.000 Å
R 因子 r_factor	0.2270
R_work r_work	0.2240
R_free r_free	0.2680

fit	/app/data/saxs_computation/hk/1hkv/1hkv.fit
pddf	/app/data/pr_computation/hk/1hkv/1hkv.pr.out
profile	/app/data/saxs_computation/hk/1hkv/1hkv.dat

mycobacterium diaminopimelate dicarboxylase (lysa)

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