SAXSdb — 8f6h

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8f6h
沉积日期 deposition_date	2022-11-16
结构标题 title	Cryo-EM structure of a Zinc-loaded asymmetrical TMD D70A mutant of the YiiP-Fab complex
关键词 keywords	Zinc transporter, cation diffusion facilitator, membrane protein, transport protein; TRANSPORT PROTEIN
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	48.24 Å
回转半径 Rg (电子) rg_electron	49.35 Å
零角强度 I(0) i0	310937000.00
分子量 molecular_weight	147930.0 kDa
排除体积 excluded_volume	186250 Å³
包络体积 envelope_volume	270440 Å³
水化壳体积 shell_volume	49725 Å³
包络直径 envelope_diameter	156.3 Å
壳层 Rg shell_rg	46.64 Å
包络 Rg envelope_rg	49.17 Å
形状 Rg shape_rg	49.35 Å
总 Rg total_rg	49.21 Å
总原子数 total_atoms	20768
残基数 n_residues	1358
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	144.7 Å
Rg (实空间) rg_real	48.42 Å
Rg 误差 (实空间) rg_real_error	1.42 Å
I(0) (实空间) i0_real	3.1090e+08
I(0) 误差 (实空间) i0_real_error	6.5410e+06
Rg (倒空间) rg_reciprocal	48.24 Å
I(0) (倒空间) i0_reciprocal	310900000.0000
解质量估计 total_estimate	0.6134
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	35.1 Å
偏度 Skewness skewness	0.224
峰度 Kurtosis kurtosis	-0.813
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16600000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.978; Stabil: 1.000; Sysdev: 0.044; Positv: 1.000; Valcen: 0.903; Smooth: 0.001

▶

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

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	Cadmium and zinc efflux pump FieF
分子量 formula_weight	32441.2 kDa
突变 mutation	D70A
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	A,B
原子数 atom_count	20768

MTQTSQYDFWVKLASRASVATALTLITIKLLAWLYSGSASMLASLTDSFADTLASIINFIAIRYAIVPAAHDHRYGHGKAEPLAALAQSAFIMGSAFLLLFYGGERLLNPSPVENATLGVVVSVVAIVLTLALVLLQKRALAATNSTVVEADSLHYKSDLFLNAAVLLALVLSQYGWWWADGLFAVLIACYIGQQAFDLGYRSIQALLDRELDEDTRQRIKLIAKEDPRVLGLHDLRTRQAGKTVFIQFHLELDGNLSLNEAHSITDTTGLRVKAAFEDAEVIIHQDPVQVEPTTQ

来源 Source

来源生物 organism	Shewanella oneidensis MR-1
NCBI 分类编号 ncbi_taxonomy_id	211586
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Fab2r light chain
分子量 formula_weight	23580.2 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,E

SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQIWSWPLITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	Fab2r heavy chain
分子量 formula_weight	25406.4 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	D,F

EISEVQLVESGGGLVQPGGSLRLSCAASGFTIYSSSIHWVRQAPGKGLEWVASIYSSSGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARQSYSGLSPRRHWSYGAMDYWGQGTLVTVFNQIKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

来源 Source

来源生物 organism	Homo sapiens
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 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	6

▼

6. 折叠分类 (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

结构域编号 domain_id	8f6hA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1510 — Alpha-lytic protease prodomain-like
同源超家族 H-superfamily homologous superfamily	10 — Cation efflux protein transmembrane domain

结构域编号 domain_id	8f6hA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1350 — Cation efflux protein, cytoplasmic domain

结构域编号 domain_id	8f6hB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1510 — Alpha-lytic protease prodomain-like
同源超家族 H-superfamily homologous superfamily	10 — Cation efflux protein transmembrane domain

结构域编号 domain_id	8f6hB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1350 — Cation efflux protein, cytoplasmic domain

结构域编号 domain_id	8f6hC01
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	8f6hC02
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	8f6hD01
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	8f6hD02
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	8f6hE01
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	8f6hE02
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	8f6hF01
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	8f6hF02
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

▶

7. 引用文献 (1)

▶

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	3.90 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	188414

fit	/app/data/saxs_computation/f6/8f6h/8f6h.fit
pddf	/app/data/pr_computation/f6/8f6h/8f6h.pr.out
profile	/app/data/saxs_computation/f6/8f6h/8f6h.dat

Cryo-EM structure of a Zinc-loaded asymmetrical TMD D70A mutant of the YiiP-Fab complex

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

6. 折叠分类 (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)