8v4p

;Crystal structure of Acetyl-CoA synthetase 2 in complex with Adenosine-5'-allylphosphate from Candida albicans ;

Method: X-RAY DIFFRACTION D_max: 126.6 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	8v4p
沉积日期 deposition_date	2023-11-29
最后修订 last_revision	2023-12-06
结构标题 title	;Crystal structure of Acetyl-CoA synthetase 2 in complex with Adenosine-5'-allylphosphate from Candida albicans ;
关键词 keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, Acetyl-coenzyme A synthetase 2, LIGASE; LIGASE
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	39.83 Å
回转半径 Rg (电子) rg_electron	39.17 Å
零角强度 I(0) i0	603325000.00
分子量 molecular_weight	201450.0 kDa
排除体积 excluded_volume	251550 Å³
包络体积 envelope_volume	309290 Å³
水化壳体积 shell_volume	64095 Å³
包络直径 envelope_diameter	128.0 Å
壳层 Rg shell_rg	46.00 Å
包络 Rg envelope_rg	39.30 Å
形状 Rg shape_rg	39.19 Å
总 Rg total_rg	39.47 Å
总原子数 total_atoms	14220
残基数 n_residues	1817
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	126.6 Å
Rg (实空间) rg_real	39.69 Å
Rg 误差 (实空间) rg_real_error	0.89 Å
I(0) (实空间) i0_real	6.0330e+08
I(0) 误差 (实空间) i0_real_error	9.5080e+06
Rg (倒空间) rg_reciprocal	39.78 Å
I(0) (倒空间) i0_reciprocal	603400000.0000
解质量估计 total_estimate	0.8950
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	44.3 Å
偏度 Skewness skewness	0.213
峰度 Kurtosis kurtosis	-0.561
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	103700000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.827

▶

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

▶

5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	Acetyl-coenzyme A synthetase 2
分子量 formula_weight	75908.4 kDa
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	14592

MHHHHHHHHENLYFQGPTEQTHNVVHEANGVKLRETPKEFFERQPNKGHIHDVNQYKQMYEQSIKDPQGFFGPLAKELLSWDHDFHTVKSGTLKNGDAAWFLGGELNASYNCVDRHAFANPDKPALICEADDEKDSHILTYGDLLREVSKVAGVLQSWGIKKGDTVAVYLPMNAQAIIAMLAIARLGAAHSVIFAGFSAGSIKDRVNDASCKALITCDEGKRGGRTTNIKKLCDEALVDCPTVEKVLVYKRTNNPEIHLTEGRDYYWDVETAKFPGYLPPVSVNSEDPLFLLYTSGSTGTPKGVVHSTAGYLLGAALSTKYIFDIHPEDILFTAGDVGWITGHTYALYGPLLLGVPTIIFEGTPAYPDYGRFWQIVEKHKATHFYVAPTALRLLRKAGEQEIAKYDLSSLRTLGSVGEPISPDIWEWYNEFVGKNQCHISDTYWQTESGSHLIAPLAGVVPNKPGSASYPFFGIDAALIDPVTGVEIEGNDAEGVLAIKDHWPSMARTVYKNHTKYMDTYMNPYPGYYFTGDGAARDHDGYYWIRGRVDDVVNVSGHRLSTAEIEAALIEDKKVSEAAVVGIHDDITGQAVIAYVALKEGNSDEDSEGLRKELVLQVRKTIGPFAAPKSVIIVQDLPKTRSGKIMRRILRKVSSNEADQLGDISTLSNPQSVEGIISAFGAQFGKK

来源 Source

来源生物 organism	Candida albicans
NCBI 分类编号 ncbi_taxonomy_id	5476
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	11

Entity 3 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 4 non-polymer

描述 description	5'-O-{(S)-hydroxy[(prop-2-en-1-yl)oxy]phosphoryl}adenosine
分子量 formula_weight	387.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 5 non-polymer

描述 description	TETRAETHYLENE GLYCOL
分子量 formula_weight	194.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 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	366

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	138.543 Å
晶胞边长 b length_b	138.543 Å
晶胞边长 c length_c	543.538 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	36

空间群 space_group	P 61 2 2
空间群编号 int_tables_number	178
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	49.510 Å
R 因子 r_factor	0.2127
R_work r_work	0.2114
R_free r_free	0.2380

fit	/app/data/saxs_computation/v4/8v4p/8v4p.fit
pddf	/app/data/pr_computation/v4/8v4p/8v4p.pr.out
profile	/app/data/saxs_computation/v4/8v4p/8v4p.dat