SAXSdb — 1w6j

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1w6j
沉积日期 deposition_date	2004-08-18
结构标题 title	Structure of human OSC in complex with Ro 48-8071
关键词 keywords	CYCLASE, CHOLESTEROL, LANOSTEROL, MONOTOPIC MEMBRANE PROTEIN, B-OCTYL-GLUCOSIDE, ISOMERASE, STEROID BIOSYNTHESIS; ISOMERASE
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	26.47 Å
回转半径 Rg (电子) rg_electron	25.40 Å
零角强度 I(0) i0	113140000.00
分子量 molecular_weight	83936.0 kDa
排除体积 excluded_volume	104900 Å³
包络体积 envelope_volume	119350 Å³
水化壳体积 shell_volume	37320 Å³
包络直径 envelope_diameter	87.6 Å
壳层 Rg shell_rg	34.36 Å
包络 Rg envelope_rg	25.70 Å
形状 Rg shape_rg	25.40 Å
总 Rg total_rg	26.28 Å
总原子数 total_atoms	5914
残基数 n_residues	727
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	81.3 Å
Rg (实空间) rg_real	26.32 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	1.1310e+08
I(0) 误差 (实空间) i0_real_error	1.6070e+06
Rg (倒空间) rg_reciprocal	26.37 Å
I(0) (倒空间) i0_reciprocal	113100000.0000
解质量估计 total_estimate	0.8996
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	33.9 Å
偏度 Skewness skewness	0.200
峰度 Kurtosis kurtosis	-0.399
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	28480000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.984

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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 (5)

Entity 1 polymer

描述 description	LANOSTEROL SYNTHASE
分子量 formula_weight	83406.6 kDa
EC 编号 ec_number	5.4.99.7
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	6330

MTEGTCLRRRGGPYKTEPATDLGRWRLNCERGRQTWTYLQDERAGREQTGLEAYALGLDTKNYFKDLPKAHTAFEGALNGMTFYVGLQAEDGHWTGDYGGPLFLLPGLLITCHVARIPLPAGYREEIVRYLRSVQLPDGGWGLHIEDKSTVFGTALNYVSLRILGVGPDDPDLVRARNILHKKGGAVAIPSWGKFWLAVLNVYSWEGLNTLFPEMWLFPDWAPAHPSTLWCHCRQVYLPMSYCYAVRLSAAEDPLVQSLRQELYVEDFASIDWLAQRNNVAPDELYTPHSWLLRVVYALLNLYEHHHSAHLRQRAVQKLYEHIVADDRFTKSISIGPISKTINMLVRWYVDGPASTAFQEHVSRIPDYLWMGLDGMKMQGTNGSQIWDTAFAIQALLEAGGHHRPEFSSCLQKAHEFLRLSQVPDNPPDYQKYYRQMRKGGFSFSTLDCGWIVSDCTAEALKAVLLLQEKCPHVTEHIPRERLCDAVAVLLNMRNPDGGFATYETKRGGHLLELLNPSEVFGDIMIDYTYVECTSAVMQALKYFHKRFPEHRAAEIRETLTQGLEFCRRQQRADGSWEGSWGVCFTYGTWFGLEAFACMGQTYRDGTACAEVSRACDFLLSRQMADGGWGEDFESCEERRYLQSAQSQIHNTCWAMMGLMAVRHPDIEAQERGVRCLLEKQLPNGDWPQENIAGVFNKSCAISYTSYRNIFPIWALGRFSQLYPERALAGHP

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	PICHIA PASTORIS

Entity 2 non-polymer

描述 description	[4-({6-[ALLYL(METHYL)AMINO]HEXYL}OXY)-2-FLUOROPHENYL](4-BROMOPHENYL)METHANONE
分子量 formula_weight	448.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	octyl beta-D-glucopyranoside
分子量 formula_weight	292.4 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 4 non-polymer

描述 description	TETRADECANE
分子量 formula_weight	198.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	416

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6. 折叠分类 (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1w6ja1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.102 — alpha/alpha toroid
超家族 Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
家族 Family family	a.102.4.2 — Terpene synthases

结构域编号 domain_id	d1w6ja2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.102 — alpha/alpha toroid
超家族 Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
家族 Family family	a.102.4.2 — Terpene synthases

CATH v4.4 (3 domains)

结构域编号 domain_id	1w6jA01
类 Class class	6 — Special
架构 Architecture architecture	20 — Other non-globular
拓扑 Topology topology	120 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1w6jA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	50 — Alpha/alpha barrel
拓扑 Topology topology	10 — Glycosyltransferase
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1w6jA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	50 — Alpha/alpha barrel
拓扑 Topology topology	10 — Glycosyltransferase
同源超家族 H-superfamily homologous superfamily	20 —

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7. 引用文献 (2)

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晶胞边长 a length_a	189.915 Å
晶胞边长 b length_b	202.424 Å
晶胞边长 c length_c	62.638 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	8

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	141.420 Å
R 因子 r_factor	0.1710
R_work r_work	0.1700
R_free r_free	0.1990

fit	/app/data/saxs_computation/w6/1w6j/1w6j.fit
pddf	/app/data/pr_computation/w6/1w6j/1w6j.pr.out
profile	/app/data/saxs_computation/w6/1w6j/1w6j.dat

Structure of human OSC in complex with Ro 48-8071

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