8t1w

Crystal structure of orphan G protein-coupled receptor 6 with bound CVN424

Method: X-RAY DIFFRACTION D_max: 96.8 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	8t1w
沉积日期 deposition_date	2023-06-04
结构标题 title	Crystal structure of orphan G protein-coupled receptor 6 with bound CVN424
关键词 keywords	Orphan GPCR, GPR6, BRIL, CVN424, inverse agonist, LCP, synchrotron, APS, 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	27.46 Å
回转半径 Rg (电子) rg_electron	27.44 Å
零角强度 I(0) i0	43120600.00
分子量 molecular_weight	34870.0 kDa
排除体积 excluded_volume	34124 Å³
包络体积 envelope_volume	59243 Å³
水化壳体积 shell_volume	20776 Å³
包络直径 envelope_diameter	101.7 Å
壳层 Rg shell_rg	30.42 Å
包络 Rg envelope_rg	28.06 Å
形状 Rg shape_rg	27.39 Å
总 Rg total_rg	27.78 Å
总原子数 total_atoms	2651
残基数 n_residues	357
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	96.8 Å
Rg (实空间) rg_real	28.01 Å
Rg 误差 (实空间) rg_real_error	0.87 Å
I(0) (实空间) i0_real	4.3120e+07
I(0) 误差 (实空间) i0_real_error	6.7070e+05
Rg (倒空间) rg_reciprocal	27.84 Å
I(0) (倒空间) i0_reciprocal	43120000.0000
解质量估计 total_estimate	0.7511
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	21.7 Å
偏度 Skewness skewness	0.704
峰度 Kurtosis kurtosis	-0.127
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6665000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.542; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.437; Smooth: 0.697

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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 (2)

Entity 1 polymer

描述 description	G-protein coupled receptor 6, Soluble cytochrome b562 chimera
分子量 formula_weight	49715.5 kDa
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	2656

MKTIIALSYIFCLVFADYKDDDDAGRAGGANGSLELSSQLSAGPPGLLLPAVNPWDVLLCVSGTVIAGENALVVALIASTPALRTPMFVLVGSLATADLLAGLGLILHFVFQYLVPSETVSLLTVGFLVASFAASVSSLLAITVDRYLSLYNPLTYYSRRTLLGVHLLLAATWTVSLGLGLLPVLGWNCLAERAACSVVRPLARSHVALLSAAFFMVFGIMLHLYVRICQVVWRHAADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLAHLAATRKGVRTLAVVLGTFGACWLPFAIYCVVGSHEDPAVYTYATLLPATLNSMINPIIYAFRNQEIQRALWLLLDGCFQSKVPFRSRSPSEVEFLEVLFQGPHHHHHHHHH

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	Homo sapiens

Entity 2 non-polymer

描述 description	1-{2-[4-(2,4-difluorophenoxy)piperidin-1-yl]-3-{[(3R)-oxolan-3-yl]amino}-7,8-dihydropyrido[3,4-b]pyrazin-6(5H)-yl}ethan-1-one
分子量 formula_weight	473.5 kDa
来源方法 src_method	syn
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	63.731 Å
晶胞边长 b length_b	63.731 Å
晶胞边长 c length_c	250.932 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	6

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	—

分辨率 resolution	3.490 Å
最低分辨率 resolution_low	46.070 Å
R 因子 r_factor	0.2929
R_work r_work	0.2913
R_free r_free	0.3219

fit	/app/data/saxs_computation/t1/8t1w/8t1w.fit
pddf	/app/data/pr_computation/t1/8t1w/8t1w.pr.out
profile	/app/data/saxs_computation/t1/8t1w/8t1w.dat

Crystal structure of orphan G protein-coupled receptor 6 with bound CVN424

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

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)