8vzc

;Crystal Structure of 2-Hydroxyacyl-CoA Lyase/Synthse ApbHACS from Alphaproteobacteria bacterium in the Complex with THDP, Formyl-CoA, and ADP ;

Method: X-RAY DIFFRACTION D_max: 116.9 Å Quality: EXCELLENT

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	8vzc
沉积日期 deposition_date	2024-02-11
最后修订 last_revision	2024-10-02
结构标题 title	;Crystal Structure of 2-Hydroxyacyl-CoA Lyase/Synthse ApbHACS from Alphaproteobacteria bacterium in the Complex with THDP, Formyl-CoA, and ADP ;
关键词 keywords	2-hydroxyacyl-CoA lyase/synthase, acyloin condensation, oxalyl-CoA decarboxylase, SBC, eBERlight, LYASE; LYASE
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	38.05 Å
回转半径 Rg (电子) rg_electron	37.16 Å
零角强度 I(0) i0	945410000.00
分子量 molecular_weight	244440.0 kDa
排除体积 excluded_volume	302650 Å³
包络体积 envelope_volume	363680 Å³
水化壳体积 shell_volume	76083 Å³
包络直径 envelope_diameter	118.8 Å
壳层 Rg shell_rg	46.92 Å
包络 Rg envelope_rg	37.24 Å
形状 Rg shape_rg	37.17 Å
总 Rg total_rg	37.60 Å
总原子数 total_atoms	17132
残基数 n_residues	2217
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	116.9 Å
Rg (实空间) rg_real	37.77 Å
Rg 误差 (实空间) rg_real_error	0.83 Å
I(0) (实空间) i0_real	9.4540e+08
I(0) 误差 (实空间) i0_real_error	1.6130e+07
Rg (倒空间) rg_reciprocal	37.95 Å
I(0) (倒空间) i0_reciprocal	945600000.0000
解质量估计 total_estimate	0.9013
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	47.3 Å
偏度 Skewness skewness	0.105
峰度 Kurtosis kurtosis	-0.571
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	390400000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.955

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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 (9)

Entity 1 polymer

描述 description	Oxalyl-CoA decarboxylase
分子量 formula_weight	59512.7 kDa
EC 编号 ec_number	4.1.1.8
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	19329

SNAMAKSEGKVNGATLMARALQQQGVQYMFGIVGFPVIPIAIAAQREGITYIGMRNEQSASYAAQAASYLTGRPQACLVVSGPGVVHALAGLANAQVNCWPMLLIGGASAIEQNGMGAFQEERQVLLASPLCKYAHQVERPERIPYYVEQAVRSALFGRPGAAYLDMPDDVILGEVEEAAVRPAATVGEPPRSLAPQENIEAALDALQSAKRPLVIVGKGMAWSRAENEVRQFIERTRLPFLATPMGKGVMPDDHPLSVGGARSHALQEADLVFLLGARFNWILHFGLPPRYSKDVRVIQLDLSAEEIGNNRQAEVALVGDGKAIVGQLNQALSSRQWFYPAETPWREAIAAKIAGNQAAVAPMIADNTSPMNYYRVYRDIAARLPRNAIIVGEGANTMDIGRTQMPNFEPRSRLDAGSYGTMGIGLGFAVAAAAVHPGRPVIAVQGDSAFGFSGMEFETAARYGMPIKVIILNNGGIGMGSPAPRDGQPGMPHALSHDARYERIAEAFGGAGFYVTDSAELGPALDAAMAFKGPAIVNIKIAATADRKPQQFNWHG

来源 Source

来源生物 organism	Alphaproteobacteria bacterium
NCBI 分类编号 ncbi_taxonomy_id	1913988
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	;3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-(hydroxymethyl)-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium ;
分子量 formula_weight	455.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	;S-{(9R,13S,15R)-17-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-9,13,15-TRIHYDROXY-10,10-DIMETHYL-13,15-DIOXIDO-4,8-DIOXO-12,14,16-TRIOXA-3,7-DIAZA-13,15-DIPHOSPHAHEPTADEC-1-YL} THIOFORMATE ;
分子量 formula_weight	795.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 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	12

Entity 7 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 8 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 9 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	2063

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7. 引用文献 (1)

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晶胞边长 a length_a	69.084 Å
晶胞边长 b length_b	102.442 Å
晶胞边长 c length_c	103.977 Å
晶胞夹角 α angle_alpha	113.83 °
晶胞夹角 β angle_beta	96.81 °
晶胞夹角 γ angle_gamma	105.45 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	1.720 Å
最低分辨率 resolution_low	38.630 Å
R 因子 r_factor	0.1634
R_work r_work	0.1616
R_free r_free	0.1976

fit	/app/data/saxs_computation/vz/8vzc/8vzc.fit
pddf	/app/data/pr_computation/vz/8vzc/8vzc.pr.out
profile	/app/data/saxs_computation/vz/8vzc/8vzc.dat