SAXSdb — 8ipt

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8ipt
沉积日期 deposition_date	2023-03-14
结构标题 title	Cryo-EM structure of heme transporter CydDC from Escherichia coli in the occluded ATP bound state
关键词 keywords	ABC transporter, Heme, TRANSPORT PROTEIN; TRANSPORT PROTEIN
实验方法 method	ELECTRON MICROSCOPY

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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	61.95 Å
回转半径 Rg (电子) rg_electron	62.20 Å
零角强度 I(0) i0	908744000.00
分子量 molecular_weight	257960.0 kDa
排除体积 excluded_volume	326080 Å³
包络体积 envelope_volume	482210 Å³
水化壳体积 shell_volume	71762 Å³
包络直径 envelope_diameter	221.8 Å
壳层 Rg shell_rg	52.18 Å
包络 Rg envelope_rg	61.68 Å
形状 Rg shape_rg	62.16 Å
总 Rg total_rg	62.04 Å
总原子数 total_atoms	18178
残基数 n_residues	2322
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	199.9 Å
Rg (实空间) rg_real	63.09 Å
Rg 误差 (实空间) rg_real_error	1.86 Å
I(0) (实空间) i0_real	9.0860e+08
I(0) 误差 (实空间) i0_real_error	1.7670e+07
Rg (倒空间) rg_reciprocal	60.90 Å
I(0) (倒空间) i0_reciprocal	905400000.0000
解质量估计 total_estimate	0.4976
解质量评级 solution_quality	SUSPICIOUS a SUSPICIOUS solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	40.0 Å
偏度 Skewness skewness	0.567
峰度 Kurtosis kurtosis	-0.573
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	62770000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.600; Stabil: 0.999; Sysdev: 0.004; Positv: 1.000; Valcen: 0.653; Smooth: 0.002

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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 (3)

Entity 1 polymer

描述 description	ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC
分子量 formula_weight	62978.9 kDa
突变 mutation	E500Q
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
原子数 atom_count	18178

MRALLPYLALYKRHKWMLSLGIVLAIVTLLASIGLLTLSGWFLSASAVAGVAGLYSFNYMLPAAGVRGAAITRTAGRYFERLVSHDATFRVLQHLRIYTFSKLLPLSPAGLARYRQGELLNRVVADVDTLDHLYLRVISPLVGAFVVIMVVTIGLSFLDFTLAFTLGGIMLLTLFLMPPLFYRAGKSTGQNLTHLRGQYRQQLTAWLQGQAELTIFGASDRYRTQLENTEIQWLEAQRRQSELTALSQAIMLLIGALAVILMLWMASGGVGGNAQPGALIALFVFCALAAFEALAPVTGAFQHLGQVIASAVRITDLTDQKPEVTFPDTQTRVADRVSLTLRDVQFTYPEQSQQALKGISLQVNAGEHIAILGRTGCGKSTLLQLLTRAWDPQQGEILLNDSPIASLNEAALRQTISVVPQRVHLFSATLRDNLLLASPGSSDEALSEILRRVGLEKLLEDAGLNSWLGEGGRQLSGGELRRLAIARALLHDAPLVLLDQPTEGLDATTESQILELLAEMMREKTVLMVTHRLRGLSRFQQIIVMDNGQIIEQGTHAELLARQGRYYQFKQGL

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 polymer

描述 description	ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD
分子量 formula_weight	65144.0 kDa
突变 mutation	E511Q
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,E

MNKSRQKELTRWLKQQSVISQRWLNISRLLGFVSGILIIAQAWFMARILQHMIMENIPREALLLPFTLLVLTFVLRAWVVWLRERVGYHAGQHIRFAIRRQVLDRLQQAGPAWIQGKPAGSWATLVLEQIDDMHDYYARYLPQMALAVSVPLLIVVAIFPSNWAAALILLGTAPLIPLFMALVGMGAADANRRNFLALARLSGHFLDRLRGMETLRIFGRGEAEIESIRSASEDFRQRTMEVLRLAFLSSGILEFFTSLSIALVAVYFGFSYLGELDFGHYDTGVTLAAGFLALILAPEFFQPLRDLGTFYHAKAQAVGAADSLKTFMETPLAHPQRGEAELALTDPLTIEAEDLFITSPEGKTLAGPLNFTLPAGQRAVLVGRSGSGKSSLLNALSGFLSYQGSLRINGIELRDLSPESWRKHLSWVGQNPQLPAATLRDNVLLARPDASEQELQAALDNAWVSEFLPLLPQGVDTPVGDQAARLSVGQAQRVAVARALLNPCSLLLLDQPAASLDAHSEQRVMEALNAASLRQTTLMVTHQLEDLADWDVIWVMQDGRIIEQGRYAELSVAGGPFATLLAHRQEEI

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	469008
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	8iptA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1560 — ABC transporter transmembrane region fold
同源超家族 H-superfamily homologous superfamily	10 — ABC transporter type 1, transmembrane domain

结构域编号 domain_id	8iptA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	8iptC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1560 — ABC transporter transmembrane region fold
同源超家族 H-superfamily homologous superfamily	10 — ABC transporter type 1, transmembrane domain

结构域编号 domain_id	8iptC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	8iptD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1560 — ABC transporter transmembrane region fold
同源超家族 H-superfamily homologous superfamily	10 — ABC transporter type 1, transmembrane domain

结构域编号 domain_id	8iptD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	8iptE01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1560 — ABC transporter transmembrane region fold
同源超家族 H-superfamily homologous superfamily	10 — ABC transporter type 1, transmembrane domain

结构域编号 domain_id	8iptE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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7. 引用文献 (1)

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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	3.50 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	119296

fit	/app/data/saxs_computation/ip/8ipt/8ipt.fit
pddf	/app/data/pr_computation/ip/8ipt/8ipt.pr.out
profile	/app/data/saxs_computation/ip/8ipt/8ipt.dat

Cryo-EM structure of heme transporter CydDC from Escherichia coli in the occluded ATP bound state

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

6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)