8g0t

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

Method: X-RAY DIFFRACTION D_max: 129.9 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	8g0t
沉积日期 deposition_date	2023-02-01
结构标题 title	Crystal Structure of Acetyl-CoA synthetase in complex with a cyclopropyl 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	41.50 Å
回转半径 Rg (电子) rg_electron	41.23 Å
零角强度 I(0) i0	697866000.00
分子量 molecular_weight	218130.0 kDa
排除体积 excluded_volume	272900 Å³
包络体积 envelope_volume	337340 Å³
水化壳体积 shell_volume	67062 Å³
包络直径 envelope_diameter	136.2 Å
壳层 Rg shell_rg	46.78 Å
包络 Rg envelope_rg	41.72 Å
形状 Rg shape_rg	41.24 Å
总 Rg total_rg	41.43 Å
总原子数 total_atoms	15380
残基数 n_residues	1971
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	129.9 Å
Rg (实空间) rg_real	41.46 Å
Rg 误差 (实空间) rg_real_error	0.91 Å
I(0) (实空间) i0_real	6.9790e+08
I(0) 误差 (实空间) i0_real_error	1.0620e+07
Rg (倒空间) rg_reciprocal	41.50 Å
I(0) (倒空间) i0_reciprocal	697900000.0000
解质量估计 total_estimate	0.8822
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	44.4 Å
偏度 Skewness skewness	0.251
峰度 Kurtosis kurtosis	-0.628
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	245100000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.631

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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	15462

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	3

Entity 3 non-polymer

描述 description	5'-O-[(R)-(cyclopropyloxy)(hydroxy)phosphoryl]adenosine
分子量 formula_weight	387.3 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	60

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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	8g0tA01
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	8g0tB01
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	8g0tC01
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	62.682 Å
晶胞边长 b length_b	84.785 Å
晶胞边长 c length_c	105.471 Å
晶胞夹角 α angle_alpha	113.29 °
晶胞夹角 β angle_beta	106.90 °
晶胞夹角 γ angle_gamma	90.96 °
晶胞分子数 Z z_pdb	3

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.450 Å
最低分辨率 resolution_low	25.270 Å
R 因子 r_factor	0.2206
R_work r_work	0.2183
R_free r_free	0.2679

fit	/app/data/saxs_computation/g0/8g0t/8g0t.fit
pddf	/app/data/pr_computation/g0/8g0t/8g0t.pr.out
profile	/app/data/saxs_computation/g0/8g0t/8g0t.dat