SAXSdb — 8fd0

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8fd0
沉积日期 deposition_date	2022-12-01
结构标题 title	Crystal structure of bovine rod opsin in complex with a nanobody
关键词 keywords	TRANSMEMBRANE PROTEIN, GPCR, NANOBODY, 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	36.11 Å
回转半径 Rg (电子) rg_electron	35.31 Å
零角强度 I(0) i0	128849000.00
分子量 molecular_weight	97185.0 kDa
排除体积 excluded_volume	123830 Å³
包络体积 envelope_volume	156450 Å³
水化壳体积 shell_volume	37237 Å³
包络直径 envelope_diameter	118.3 Å
壳层 Rg shell_rg	40.86 Å
包络 Rg envelope_rg	35.32 Å
形状 Rg shape_rg	35.25 Å
总 Rg total_rg	35.94 Å
总原子数 total_atoms	6830
残基数 n_residues	845
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	117.4 Å
Rg (实空间) rg_real	36.08 Å
Rg 误差 (实空间) rg_real_error	1.03 Å
I(0) (实空间) i0_real	1.2880e+08
I(0) 误差 (实空间) i0_real_error	2.3360e+06
Rg (倒空间) rg_reciprocal	36.10 Å
I(0) (倒空间) i0_reciprocal	128900000.0000
解质量估计 total_estimate	0.8141
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	50.7 Å
偏度 Skewness skewness	0.135
峰度 Kurtosis kurtosis	-0.761
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	14370000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.000

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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 (6)

Entity 1 polymer

描述 description	Rhodopsin
分子量 formula_weight	39031.5 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	6830

MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Entity 2 polymer

描述 description	Nanobody Nb2
分子量 formula_weight	13849.4 kDa
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	C,D

QVQLVESGGGLVQPGGSLRLSCAASGFTFSKYAMNWVRQPPGKGLEWVSGIRPSGDNPTYADSVEGRFTIIRDNDKKMVYLQMTSLKTEDTAVYYCTRGYGTMTIEGQGTQVTVSSHHHHHHEPEA

来源 Source

来源生物 organism	Lama glama
通用名 common_name	llama
NCBI 分类编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli

Entity 3 branched

描述 description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-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	1114.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 branched

描述 description	beta-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 5 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-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	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 6 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	1

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6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id	8fd0C01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	8fd0D01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

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7. 引用文献 (1)

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晶胞边长 a length_a	120.065 Å
晶胞边长 b length_b	120.065 Å
晶胞边长 c length_c	230.943 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	12

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	3.710 Å
最低分辨率 resolution_low	47.410 Å
R 因子 r_factor	0.2921
R_work r_work	0.2919
R_free r_free	0.2953

fit	/app/data/saxs_computation/fd/8fd0/8fd0.fit
pddf	/app/data/pr_computation/fd/8fd0/8fd0.pr.out
profile	/app/data/saxs_computation/fd/8fd0/8fd0.dat

Crystal structure of bovine rod opsin in complex with a nanobody

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 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 branched

Entity 4 branched

Entity 5 branched

Entity 6 branched

6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)