1l9h

Crystal structure of bovine rhodopsin at 2.6 angstroms RESOLUTION

Method: X-RAY DIFFRACTION D_max: 88.0 Å Quality: EXCELLENT

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1l9h
沉积日期 deposition_date	2002-03-23
结构标题 title	Crystal structure of bovine rhodopsin at 2.6 angstroms RESOLUTION
关键词 keywords	G PROTEIN-COUPLED RECEPTOR, MEMBRANE PROTEIN, RETINAL PROTEIN, PHOTORECEPTOR, SIGNALING PROTEIN; SIGNALING PROTEIN
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	28.82 Å
回转半径 Rg (电子) rg_electron	27.20 Å
零角强度 I(0) i0	87437800.00
分子量 molecular_weight	80523.0 kDa
排除体积 excluded_volume	103060 Å³
包络体积 envelope_volume	117740 Å³
水化壳体积 shell_volume	35177 Å³
包络直径 envelope_diameter	90.3 Å
壳层 Rg shell_rg	35.45 Å
包络 Rg envelope_rg	27.43 Å
形状 Rg shape_rg	27.22 Å
总 Rg total_rg	28.01 Å
总原子数 total_atoms	5558
残基数 n_residues	641
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	88.0 Å
Rg (实空间) rg_real	28.69 Å
Rg 误差 (实空间) rg_real_error	0.76 Å
I(0) (实空间) i0_real	8.7440e+07
I(0) 误差 (实空间) i0_real_error	1.4120e+06
Rg (倒空间) rg_reciprocal	28.75 Å
I(0) (倒空间) i0_reciprocal	87440000.0000
解质量估计 total_estimate	0.9116
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	43.2 Å
偏度 Skewness skewness	0.086
峰度 Kurtosis kurtosis	-0.653
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	19600000.0000
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: 0.953; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.992

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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 (11)

Entity 1 polymer

描述 description	rhodopsin
分子量 formula_weight	39057.5 kDa
来源方法 src_method	nat
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	5584

XMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Entity 2 branched

描述 description	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 4 branched

描述 description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	748.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	nonyl beta-D-glucopyranoside
分子量 formula_weight	306.4 kDa
来源方法 src_method	man
拷贝数 entity_count	7

Entity 6 non-polymer

描述 description	MERCURY (II) ION
分子量 formula_weight	200.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 7 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 8 non-polymer

描述 description	HEPTANE-1,2,3-TRIOL
分子量 formula_weight	148.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 9 non-polymer

描述 description	PALMITIC ACID
分子量 formula_weight	256.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 10 non-polymer

描述 description	RETINAL
分子量 formula_weight	284.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 11 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	26

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1l9ha_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.13 — Class A G protein-coupled receptor (GPCR)-like
超家族 Superfamily superfamily	f.13.1 — Class A G protein-coupled receptor (GPCR)-like
家族 Family family	f.13.1.2 — Rhodopsin-like

结构域编号 domain_id	d1l9hb_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.13 — Class A G protein-coupled receptor (GPCR)-like
超家族 Superfamily superfamily	f.13.1 — Class A G protein-coupled receptor (GPCR)-like
家族 Family family	f.13.1.2 — Rhodopsin-like

CATH v4.4 (2 domains)

结构域编号 domain_id	1l9hA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1070 — Rhopdopsin 7-helix transmembrane proteins
同源超家族 H-superfamily homologous superfamily	10 — Rhodopsin 7-helix transmembrane proteins

结构域编号 domain_id	1l9hB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1070 — Rhopdopsin 7-helix transmembrane proteins
同源超家族 H-superfamily homologous superfamily	10 — Rhodopsin 7-helix transmembrane proteins

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7. 引用文献 (1)

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晶胞边长 a length_a	96.745 Å
晶胞边长 b length_b	96.745 Å
晶胞边长 c length_c	149.300 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	P 41
空间群编号 int_tables_number	76
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.1880
R_free r_free	0.2250

fit	/app/data/saxs_computation/l9/1l9h/1l9h.fit
pddf	/app/data/pr_computation/l9/1l9h/1l9h.pr.out
profile	/app/data/saxs_computation/l9/1l9h/1l9h.dat