8v4r

Crystal structure of Acetyl-CoA synthetase 2 in complex with AMP and CoA from Candida albicans

Method: X-RAY DIFFRACTION D_max: 122.6 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8v4r
沉积日期 deposition_date	2023-11-29
结构标题 title	Crystal structure of Acetyl-CoA synthetase 2 in complex with AMP and CoA 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

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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	39.99 Å
回转半径 Rg (电子) rg_electron	39.33 Å
零角强度 I(0) i0	627763000.00
分子量 molecular_weight	206500.0 kDa
排除体积 excluded_volume	258290 Å³
包络体积 envelope_volume	317220 Å³
水化壳体积 shell_volume	65038 Å³
包络直径 envelope_diameter	131.2 Å
壳层 Rg shell_rg	46.49 Å
包络 Rg envelope_rg	39.57 Å
形状 Rg shape_rg	39.32 Å
总 Rg total_rg	39.69 Å
总原子数 total_atoms	14582
残基数 n_residues	1852
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	122.6 Å
Rg (实空间) rg_real	39.88 Å
Rg 误差 (实空间) rg_real_error	0.63 Å
I(0) (实空间) i0_real	6.2780e+08
I(0) 误差 (实空间) i0_real_error	9.4570e+06
Rg (倒空间) rg_reciprocal	39.99 Å
I(0) (倒空间) i0_reciprocal	627800000.0000
解质量估计 total_estimate	0.8951
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	42.9 Å
偏度 Skewness skewness	0.153
峰度 Kurtosis kurtosis	-0.672
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	218000000.0000
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: 0.961; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.751

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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 (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	14623

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	ADENOSINE MONOPHOSPHATE
分子量 formula_weight	347.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	COENZYME A
分子量 formula_weight	767.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 4 non-polymer

描述 description	ACETIC ACID
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 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	41

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7. 引用文献 (1)

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晶胞边长 a length_a	139.407 Å
晶胞边长 b length_b	139.407 Å
晶胞边长 c length_c	542.252 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	2.700 Å
最低分辨率 resolution_low	49.460 Å
R 因子 r_factor	0.2075
R_work r_work	0.2063
R_free r_free	0.2309

fit	/app/data/saxs_computation/v4/8v4r/8v4r.fit
pddf	/app/data/pr_computation/v4/8v4r/8v4r.pr.out
profile	/app/data/saxs_computation/v4/8v4r/8v4r.dat