8g0u

Crystal Structure of Acetyl-CoA synthetase in complex with an isopropyl ester AMP inhibitor from Cryptococcus neoformans H99

Method: X-RAY DIFFRACTION D_max: 129.2 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	8g0u
沉积日期 deposition_date	2023-02-01
结构标题 title	Crystal Structure of Acetyl-CoA synthetase in complex with an isopropyl ester AMP inhibitor from Cryptococcus neoformans H99
关键词 keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, 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	39.46 Å
回转半径 Rg (电子) rg_electron	39.08 Å
零角强度 I(0) i0	578357000.00
分子量 molecular_weight	196670.0 kDa
排除体积 excluded_volume	245400 Å³
包络体积 envelope_volume	296960 Å³
水化壳体积 shell_volume	62303 Å³
包络直径 envelope_diameter	135.9 Å
壳层 Rg shell_rg	45.33 Å
包络 Rg envelope_rg	39.43 Å
形状 Rg shape_rg	39.11 Å
总 Rg total_rg	39.30 Å
总原子数 total_atoms	13869
残基数 n_residues	1784
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	129.2 Å
Rg (实空间) rg_real	39.43 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	5.7840e+08
I(0) 误差 (实空间) i0_real_error	8.0280e+06
Rg (倒空间) rg_reciprocal	39.46 Å
I(0) (倒空间) i0_reciprocal	578400000.0000
解质量估计 total_estimate	0.8885
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	42.0 Å
偏度 Skewness skewness	0.300
峰度 Kurtosis kurtosis	-0.498
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	162400000.0000
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: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.872

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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 (4)

Entity 1 polymer

描述 description	Acetyl-coenzyme A synthetase
分子量 formula_weight	77475.8 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	15010

MHHHHHHHHENLYFQGKTEVAPGVHHVHPLPDSVPESEDLFAPPPRMQGKEGRPKPHIGPNYESYVKEWAKTVGPNSDEWWAAKARETLDWYDDFKTVRAGGFEHGDVQWFPEGTLNAAYNCLDRHYYKNPKKTAIIYEADEPSESREVSYEELMQETCRVANVLKSYGVKKGDAVSIYLPMTWQAAAAFLACARIGAIHSAVFAGFSAESLRDRVNDCECKVLITTDEGRRGGKTIATKQIVDAALQQCPLVENVLVLRRTGNKVPMTEGRDKWWDEECAKMPAYCPCERMASEDPLFILYTSGSTGKPKGVVHSTAGYLLGTALTLKYVFDAHPDDRFACMADIGWITGHSYIIYGPLANGITTAVFESTPVYPTPSRYWDFVDKWKATQLYTAPTAIRLLRRMGEDHVKNHDLSSLRVLGSVGEPINPEAWHWYNDFAGKNQCAIVDTYWMTETGSISIAPLPGAISTKPGSATFPFFGMDVDIIDPQTGQVLEGNDVEGVLVARRPWPSIARTVYRDHKRYLETYMKPYPGYFFFGDGAARDYDGYMWIKGRVDDVINVSGHRLSTAEVESALILHKGVAETAVVGCADDLTGQAVYAFVTMKPEFDLKATKEADLSKELAIQVRKVIGPFAAPKKIYLVSDLPKTRSGKIMRRVLRKIVAGEGDQLGDLSSIADPQIVEEVKQKVTGSA

来源 Source

来源生物 organism	Cryptococcus neoformans
NCBI 分类编号 ncbi_taxonomy_id	5207
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 3 non-polymer

描述 description	5'-O-{(R)-hydroxy[(propan-2-yl)oxy]phosphoryl}adenosine
分子量 formula_weight	389.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 4 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	979

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6. 折叠分类 (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

结构域编号 domain_id	8g0uA01
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	12780 — ANL, N-terminal domain

结构域编号 domain_id	8g0uB01
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	12780 — ANL, N-terminal domain

结构域编号 domain_id	8g0uC01
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	12780 — ANL, N-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	71.879 Å
晶胞边长 b length_b	183.779 Å
晶胞边长 c length_c	84.076 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	92.98 °
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	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	35.890 Å
R 因子 r_factor	0.1750
R_work r_work	0.1735
R_free r_free	0.2037

fit	/app/data/saxs_computation/g0/8g0u/8g0u.fit
pddf	/app/data/pr_computation/g0/8g0u/8g0u.pr.out
profile	/app/data/saxs_computation/g0/8g0u/8g0u.dat