8r4d

Focused map on the Roc-COR domains of the Roco protein from C. tepidum in the GTP state bound to the activating Nanobody NbRoco1

Method: ELECTRON MICROSCOPY D_max: 86.0 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8r4d
沉积日期 deposition_date	2023-11-13
结构标题 title	Focused map on the Roc-COR domains of the Roco protein from C. tepidum in the GTP state bound to the activating Nanobody NbRoco1
关键词 keywords	;GTPase, Nanobody, Parkinson's Disease, Allostery activator, HYDROLASE ;; HYDROLASE
实验方法 method	ELECTRON MICROSCOPY

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	26.54 Å
回转半径 Rg (电子) rg_electron	25.56 Å
零角强度 I(0) i0	44563800.00
分子量 molecular_weight	50629.0 kDa
排除体积 excluded_volume	62841 Å³
包络体积 envelope_volume	83087 Å³
水化壳体积 shell_volume	27761 Å³
包络直径 envelope_diameter	89.9 Å
壳层 Rg shell_rg	32.16 Å
包络 Rg envelope_rg	25.57 Å
形状 Rg shape_rg	25.54 Å
总 Rg total_rg	26.37 Å
总原子数 total_atoms	3573
残基数 n_residues	478
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	86.0 Å
Rg (实空间) rg_real	26.54 Å
Rg 误差 (实空间) rg_real_error	0.56 Å
I(0) (实空间) i0_real	4.4560e+07
I(0) 误差 (实空间) i0_real_error	6.7080e+05
Rg (倒空间) rg_reciprocal	26.54 Å
I(0) (倒空间) i0_reciprocal	44560000.0000
解质量估计 total_estimate	0.8967
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	31.5 Å
偏度 Skewness skewness	0.360
峰度 Kurtosis kurtosis	-0.274
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	12560000.0000
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: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.971

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	Rab family protein
分子量 formula_weight	124313.5 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	3573

GAMGSMSDLDVIRQIEQELGMQLEPVDKLKWYSKGYKLDKDQRVTAIGLYDCGSDTLDRIIQPLESLKSLSELSLSSNQITDISPLASLNSLSMLWLDRNQITDIAPLASLNSLSMLWLFGNKISDIAPLESLKSLTELQLSSNQITDIAPLASLKSLTELSLSGNNISDIAPLESLKSLTELSLSSNQITDIAPLASLKSLTELSLSSNQISDIAPLESLKSLTELQLSRNQISDIAPLESLKSLTELQLSSNQITDIAPLASLKSLTELQLSRNQISDIAPLESLNSLSKLWLNGNQITDIAPLASLNSLTELELSSNQITDIAPLASLKSLSTLWLSSNQISDIAPLASLESLSELSLSSNQISDISPLASLNSLTGFDVRRNPIKRLPETITGFDMEILWNDFSSSGFITFFDNPLESPPPEIVKQGKEAVRQYFQSIEEARSKGEALVHLQEIKVHLIGDGMAGKTSLLKQLIGETFDPKESQTHGLNVVTKQAPNIKGLENDDELKECLFHFWDFGGQEIMHASHQFFMTRSSVYMLLLDSRTDSNKHYWLRHIEKYGGKSPVIVVMNKIDENPSYNIEQKKINERFPAIENRFHRISCKNGDGVESIAKSLKSAVLHPDSIYGTPLAPSWIKVKEKLVEATTAQRYLNRTEVEKICNDSGITDPGERKTLLGYLNNLGIVLYFEALDLSEIYVLDPHWVTIGVYRIINSSKTKNGHLNTSALGYILNEEQIRCDEYDPAKNNKFTYTLLEQRYLLDIMKQFELCYDEGKGLFIIPSNLPTQIDNEPEITEGEPLRFIMKYDYLPSTIIPRLMIAMQHQILDRMQWRYGMVLKSQDHEGALAKVVAETKDSTITIAIQGEPRCKREYLSIIWYEIKKINANFTNLDVKEFIPLPGHPDELVEYKELLGLEKMGRDEYVSGKLEKVFSVSKMLDSVISKEERNKERLMGDINIKLENIGNPTIPIHQQVEVNVSQETVQHVENLQGFFENLKADILREAELEIDDPKERKRLANELELAENAITKMDAAVKSGKNKLKPDVKDRLGEFIDNLANENSRLRKGIALVMNGAEKVQKLARYYNNVAPFFDLPSVPPVLLGKEKT

来源 Source

来源生物 organism	Chlorobaculum tepidum
NCBI 分类编号 ncbi_taxonomy_id	1097
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	NbRoco1
分子量 formula_weight	15206.7 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	B

QVQLQESGGGLVQAGGSLRLSCANSGLTFSTYTMGWFRQAPGKEREFVAAIRWSGTSTYYQDHADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAASRLRAGVKAPSEYDYWGQGTQVTVSSHHHHHHEPEA

来源 Source

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

Entity 3 non-polymer

描述 description	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
分子量 formula_weight	539.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

▶

7. 引用文献 (2)

▶

晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	3.88 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	38260

fit	/app/data/saxs_computation/r4/8r4d/8r4d.fit
pddf	/app/data/pr_computation/r4/8r4d/8r4d.pr.out
profile	/app/data/saxs_computation/r4/8r4d/8r4d.dat

Focused map on the Roc-COR domains of the Roco protein from C. tepidum in the GTP state bound to the activating Nanobody NbRoco1

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)