SAXSdb — 1r7i

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1r7i
沉积日期 deposition_date	2003-10-21
结构标题 title	HMG-CoA Reductase from P. mevalonii, native structure at 2.2 angstroms resolution.
关键词 keywords	4-ELECTRON OXIDO-REDUCTASE, 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	26.92 Å
回转半径 Rg (电子) rg_electron	25.71 Å
零角强度 I(0) i0	104803000.00
分子量 molecular_weight	79439.0 kDa
排除体积 excluded_volume	99178 Å³
包络体积 envelope_volume	115210 Å³
水化壳体积 shell_volume	35996 Å³
包络直径 envelope_diameter	83.5 Å
壳层 Rg shell_rg	34.38 Å
包络 Rg envelope_rg	26.00 Å
形状 Rg shape_rg	25.72 Å
总 Rg total_rg	26.53 Å
总原子数 total_atoms	5570
残基数 n_residues	747
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	79.3 Å
Rg (实空间) rg_real	26.75 Å
Rg 误差 (实空间) rg_real_error	0.32 Å
I(0) (实空间) i0_real	1.0480e+08
I(0) 误差 (实空间) i0_real_error	1.0950e+06
Rg (倒空间) rg_reciprocal	26.80 Å
I(0) (倒空间) i0_reciprocal	104800000.0000
解质量估计 total_estimate	0.9130
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	33.6 Å
偏度 Skewness skewness	0.126
峰度 Kurtosis kurtosis	-0.544
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	23950000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.971; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.965

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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-hydroxy-3-methylglutaryl-coenzyme A reductase
分子量 formula_weight	45641.2 kDa
EC 编号 ec_number	1.1.1.88
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	5833

MSLDSRLPAFRNLSPAARLDHIGQLLGLSHDDVSLLANAGALPMDIANGMIENVIGTFELPYAVASNFQINGRDVLVPLVVEEPSIVAAASYMAKLARANGGFTTSSSAPLMHAQVQIVGIQDPLNARLSLLRRKDEIIELANRKDQLLNSLGGGCRDIEVHTFADTPRGPMLVAHLIVDVRDAMGANTVNTMAEAVAPLMEAITGGQVRLRILSNLADLRLARAQVRITPQQLETAEFSGEAVIEGILDAYAFAAVDPYRAATHNKGIMNGIDPLIVATGNDWRAVEAGAHAYACRSGHYGSLTTWEKDNNGHLVGTLEMPMPVGLVGGATKTHPLAQLSLRILGVKTAQALAEIAVAVGLAQNLGAMRALATEGIQRGHMALHARNIAVVAGARGDEVDWVARQLVEYHDVRADRAVALLKQKRGQ

来源 Source

来源生物 organism	Pseudomonas mevalonii
NCBI 分类编号 ncbi_taxonomy_id	32044
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	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	263

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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	d1r7ia1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.20 — NAD-binding domain of HMG-CoA reductase
家族 Family family	d.58.20.1 — NAD-binding domain of HMG-CoA reductase

结构域编号 domain_id	d1r7ia2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.179 — Substrate-binding domain of HMG-CoA reductase
超家族 Superfamily superfamily	d.179.1 — Substrate-binding domain of HMG-CoA reductase
家族 Family family	d.179.1.1 — Substrate-binding domain of HMG-CoA reductase

结构域编号 domain_id	d1r7ib1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.20 — NAD-binding domain of HMG-CoA reductase
家族 Family family	d.58.20.1 — NAD-binding domain of HMG-CoA reductase

结构域编号 domain_id	d1r7ib2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.179 — Substrate-binding domain of HMG-CoA reductase
超家族 Superfamily superfamily	d.179.1 — Substrate-binding domain of HMG-CoA reductase
家族 Family family	d.179.1.1 — Substrate-binding domain of HMG-CoA reductase

CATH v4.4 (4 domains)

结构域编号 domain_id	1r7iA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	420 — Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain

结构域编号 domain_id	1r7iA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	770 — 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2

结构域编号 domain_id	1r7iB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	420 — Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain

结构域编号 domain_id	1r7iB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	770 — 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	226.186 Å
晶胞边长 b length_b	226.186 Å
晶胞边长 c length_c	226.186 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	96

空间群 space_group	I 41 3 2
空间群编号 int_tables_number	214
晶系 crystal_system	—

分辨率 resolution	2.210 Å
最低分辨率 resolution_low	26.660 Å
R 因子 r_factor	0.2560
R_work r_work	0.2560
R_free r_free	0.2700

fit	/app/data/saxs_computation/r7/1r7i/1r7i.fit
pddf	/app/data/pr_computation/r7/1r7i/1r7i.pr.out
profile	/app/data/saxs_computation/r7/1r7i/1r7i.dat

HMG-CoA Reductase from P. mevalonii, native structure at 2.2 angstroms resolution.

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