SAXSdb — 1zsv

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1zsv
沉积日期 deposition_date	2005-05-25
结构标题 title	Crystal structure of human NADP-dependent leukotriene B4 12-hydroxydehydrogenase
关键词 keywords	;medium-chain dehydrogenase/reductase family, leukotriene B4, human, Structural Genomics, Structural Genomics Consortium, SGC, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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	36.61 Å
回转半径 Rg (电子) rg_electron	36.38 Å
零角强度 I(0) i0	273545000.00
分子量 molecular_weight	140600.0 kDa
排除体积 excluded_volume	178650 Å³
包络体积 envelope_volume	230000 Å³
水化壳体积 shell_volume	52151 Å³
包络直径 envelope_diameter	122.0 Å
壳层 Rg shell_rg	43.26 Å
包络 Rg envelope_rg	35.91 Å
形状 Rg shape_rg	36.35 Å
总 Rg total_rg	36.93 Å
总原子数 total_atoms	9856
残基数 n_residues	1312
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	118.1 Å
Rg (实空间) rg_real	36.49 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	2.7350e+08
I(0) 误差 (实空间) i0_real_error	4.5110e+06
Rg (倒空间) rg_reciprocal	36.56 Å
I(0) (倒空间) i0_reciprocal	273600000.0000
解质量估计 total_estimate	0.8932
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	46.7 Å
偏度 Skewness skewness	0.212
峰度 Kurtosis kurtosis	-0.418
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	45920000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.878

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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	NADP-dependent leukotriene B4 12-hydroxydehydrogenase
分子量 formula_weight	38229.2 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	10171

MHHHHHHSSGVDLGTENLYFQSMTKTWTLKKHFVGYPTNSDFELKTSELPPLKNGEVLLEALFLTVDPYMRVAAKRLKEGDTMMGQQVAKVVESKNVALPKGTIVLASPGWTTHSISDGKDLEKLLTEWPDTIPLSLALGTVGMPGLTAYFGLLEICGVKGGETVMVNAAAGAVGSVVGQIAKLKGCKVVGAVGSDEKVAYLQKLGFDVVFNYKTVESLEETLKKASPDGYDCYFDNVGGEFSNTVIGQMKKFGRIAICGAISTYNRTGPLPPGPPPEIVIYQELRMEAFVVYRWQGDARQKALKDLLKWVLEGKIQYKEYIIEGFENMPAAFMGMLKGDNLGKTIVKA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
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	22

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	315

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6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	1zsvA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

结构域编号 domain_id	1zsvA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1zsvB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

结构域编号 domain_id	1zsvB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1zsvC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

结构域编号 domain_id	1zsvC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1zsvD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

结构域编号 domain_id	1zsvD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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7. 引用文献 (1)

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晶胞边长 a length_a	92.543 Å
晶胞边长 b length_b	92.543 Å
晶胞边长 c length_c	202.770 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 43
空间群编号 int_tables_number	78
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	62.300 Å
R 因子 r_factor	0.1969
R_work r_work	0.1951
R_free r_free	0.2493

fit	/app/data/saxs_computation/zs/1zsv/1zsv.fit
pddf	/app/data/pr_computation/zs/1zsv/1zsv.pr.out
profile	/app/data/saxs_computation/zs/1zsv/1zsv.dat

Crystal structure of human NADP-dependent leukotriene B4 12-hydroxydehydrogenase

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