2i37

Crystal structure of a photoactivated rhodopsin

Method: X-RAY DIFFRACTION D_max: 155.0 Å Quality: GOOD

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	2i37
沉积日期 deposition_date	2006-08-17
结构标题 title	Crystal structure of a photoactivated rhodopsin
关键词 keywords	trans-membrane protein, GPCR, MEMBRANE PROTEIN; MEMBRANE 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	42.59 Å
回转半径 Rg (电子) rg_electron	42.95 Å
零角强度 I(0) i0	156963000.00
分子量 molecular_weight	111080.0 kDa
排除体积 excluded_volume	142440 Å³
包络体积 envelope_volume	199840 Å³
水化壳体积 shell_volume	41801 Å³
包络直径 envelope_diameter	162.4 Å
壳层 Rg shell_rg	43.39 Å
包络 Rg envelope_rg	43.71 Å
形状 Rg shape_rg	42.86 Å
总 Rg total_rg	43.32 Å
总原子数 total_atoms	7814
残基数 n_residues	954
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	155.0 Å
Rg (实空间) rg_real	43.05 Å
Rg 误差 (实空间) rg_real_error	1.99 Å
I(0) (实空间) i0_real	1.5700e+08
I(0) 误差 (实空间) i0_real_error	3.2640e+06
Rg (倒空间) rg_reciprocal	42.60 Å
I(0) (倒空间) i0_reciprocal	156900000.0000
解质量估计 total_estimate	0.7940
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	41.9 Å
偏度 Skewness skewness	0.547
峰度 Kurtosis kurtosis	-0.318
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13310000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.635; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.597; Smooth: 0.816

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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	Rhodopsin
分子量 formula_weight	39057.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	7814

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	3

Entity 4 branched

描述 description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-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	951.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 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

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7. 引用文献 (1)

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晶胞边长 a length_a	161.245 Å
晶胞边长 b length_b	161.245 Å
晶胞边长 c length_c	143.442 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	120.00 °
晶胞分子数 Z z_pdb	18

空间群 space_group	P 31 1 2
空间群编号 int_tables_number	151
晶系 crystal_system	—

分辨率 resolution	4.150 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.3780
R_work r_work	0.3770
R_free r_free	0.3820

fit	/app/data/saxs_computation/i3/2i37/2i37.fit
pddf	/app/data/pr_computation/i3/2i37/2i37.pr.out
profile	/app/data/saxs_computation/i3/2i37/2i37.dat

Crystal structure of a photoactivated rhodopsin

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