8igu

Hexameric Ring Complex of Engineered V1-ATPase: A3(De)3_empty

Method: X-RAY DIFFRACTION D_max: 140.3 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	8igu
沉积日期 deposition_date	2023-02-21
结构标题 title	Hexameric Ring Complex of Engineered V1-ATPase: A3(De)3_empty
关键词 keywords	Computational Design, Rotary Molecular Motor, Complex, MOTOR PROTEIN; MOTOR 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	45.77 Å
回转半径 Rg (电子) rg_electron	44.94 Å
零角强度 I(0) i0	1687850000.00
分子量 molecular_weight	341990.0 kDa
排除体积 excluded_volume	428270 Å³
包络体积 envelope_volume	588510 Å³
水化壳体积 shell_volume	102390 Å³
包络直径 envelope_diameter	139.6 Å
壳层 Rg shell_rg	55.14 Å
包络 Rg envelope_rg	43.91 Å
形状 Rg shape_rg	44.94 Å
总 Rg total_rg	45.32 Å
总原子数 total_atoms	24028
残基数 n_residues	3082
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	140.3 Å
Rg (实空间) rg_real	45.40 Å
Rg 误差 (实空间) rg_real_error	0.77 Å
I(0) (实空间) i0_real	1.6880e+09
I(0) 误差 (实空间) i0_real_error	3.0310e+07
Rg (倒空间) rg_reciprocal	45.77 Å
I(0) (倒空间) i0_reciprocal	1689000000.0000
解质量估计 total_estimate	0.8225
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	61.9 Å
偏度 Skewness skewness	0.021
峰度 Kurtosis kurtosis	-0.578
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	294900000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; 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 (3)

Entity 1 polymer

描述 description	V-type sodium ATPase catalytic subunit A
分子量 formula_weight	66059.5 kDa
EC 编号 ec_number	7.2.2.1
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	24292

SSGMQIGKIIKVSGPLVMAENMSEASIQDMCLVGDLGVIGEIIEMRQDVASIQVYEETSGIGPGEPVRSTGEALSVELGPGIISQMFDGIQRPLDTFMEVTQSNFLGRGVQLPALDHEKQWWFEATIEEGTEVSAGDIIGYVDETKIIQHKIMVPNGIKGTVQKIESGSFTIDDPICVIETEQGLKELTMMQKWPVRRGRPIKQKLNPDVPMITGQRVIDTFFPVTKGGAAAVPGPFGAGKTVVQHQIAKWSDVDLVVYVGCGERGNEMTDVVNEFPELIDPNTGESLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVAIMADSTSRWAEALREMSGRLEEMPGDEGYPAYLGSRLAEYYERSGRVIALGSDQREGSITAISAVSPSGGDISEPVTQNTLRVVKVFWGLDSSLAQKRHFPSINWIQSYSLYSTEVGRYMDQILQQDWSDMVTEGMRILQEEEQLNEIVRLVGIDSLSDNDRLTLEVAKSIREDYLQQNAFDDVDTFTSREKQFNMLKVILTFGKEARKALSLGAYFNEIMEGTVAVRERISRSKYIPEEELAKISSINEEIKETIQLIVSEGGMTDD

来源 Source

来源生物 organism	Enterococcus hirae ATCC 9790
NCBI 分类编号 ncbi_taxonomy_id	768486
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	V-type sodium ATPase subunit B
分子量 formula_weight	51017.2 kDa
突变 mutation	S151G, G152P, S153P, L155A, P156G, G157K, K158S, E159A, T248E, Q339S
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,E,F

MIKEYRTIKEVVGPLMAVEKVSGVKYEELIEVRMQNGEIRRGQVLEVQEDKAMVQIFEGTSGINLKNSSVRFLGHPLQLGVSEDMIGRVFDGLGRPKDNGPEILPEKYLDINGEVINPIARDYPDEFIQTGISAIDHLNTLVRGQKLPVFGPPGAGKSALAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIERIATPRMALTAAEYLAYEKGMHVLVIMEDMTNYAEALREISAARREVPGRRGYPGYLYTNLATLFERAGRIRGLKGSVTQIPILTMPEDDKTHPIPDLTGYITEGQIILTRELYKSGISPPIDVLPSLSRLKDKGTGAGKTREDHAATMNQLFAAYAQGKQAKELAVVLGESALSDIDKIYAKFAERFENEYVNQGFYTNRTITETLDLGWELLAMLPRTELKRIKDDLLDKYLPEGK

来源 Source

来源生物 organism	Enterococcus hirae ATCC 9790
NCBI 分类编号 ncbi_taxonomy_id	768486
宿主生物 host_organism	Escherichia coli

Entity 3 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	253

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7. 引用文献 (1)

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晶胞边长 a length_a	122.449 Å
晶胞边长 b length_b	122.653 Å
晶胞边长 c length_c	128.704 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.74 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	monoclinic

分辨率 resolution	2.770 Å
最低分辨率 resolution_low	44.640 Å
R 因子 r_factor	0.2187
R_work r_work	0.2165
R_free r_free	0.2624

fit	/app/data/saxs_computation/ig/8igu/8igu.fit
pddf	/app/data/pr_computation/ig/8igu/8igu.pr.out
profile	/app/data/saxs_computation/ig/8igu/8igu.dat

Hexameric Ring Complex of Engineered V1-ATPase: A3(De)3_empty

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)