8vzd

;Crystal Structure of 2-Hydroxyacyl-CoA lyase/synthase TbHACS from Thermoflexaceae bacterium in the Complex with THDP, Formyl-CoA and ADP ;

Method: X-RAY DIFFRACTION D_max: 108.3 Å Quality: REASONABLE

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	8vzd
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/synthase TbHACS from Thermoflexaceae bacterium in the Complex with THDP, Formyl-CoA and ADP ;
关键词 keywords	2-hydroxyacyl-CoA lyase/synthase, Oxalyly-CoA decarboxylase, acyloin condensation, 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	33.08 Å
回转半径 Rg (电子) rg_electron	32.52 Å
零角强度 I(0) i0	238641000.00
分子量 molecular_weight	121620.0 kDa
排除体积 excluded_volume	151200 Å³
包络体积 envelope_volume	184100 Å³
水化壳体积 shell_volume	46395 Å³
包络直径 envelope_diameter	114.2 Å
壳层 Rg shell_rg	39.90 Å
包络 Rg envelope_rg	32.62 Å
形状 Rg shape_rg	32.53 Å
总 Rg total_rg	33.04 Å
总原子数 total_atoms	8532
残基数 n_residues	1098
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	108.3 Å
Rg (实空间) rg_real	33.06 Å
Rg 误差 (实空间) rg_real_error	0.86 Å
I(0) (实空间) i0_real	2.3860e+08
I(0) 误差 (实空间) i0_real_error	4.3610e+06
Rg (倒空间) rg_reciprocal	33.07 Å
I(0) (倒空间) i0_reciprocal	238600000.0000
解质量估计 total_estimate	0.6784
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	42.9 Å
偏度 Skewness skewness	0.355
峰度 Kurtosis kurtosis	-0.243
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	123200000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.996; Smooth: 0.767

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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 (8)

Entity 1 polymer

描述 description	2-Hydroxyacyl-CoA Lyase/Synthase TbHACS
分子量 formula_weight	59060.0 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	9071

MATITGAQIVARALKQQGVEHMFGIVGIPVIPIAAAAQREGIKFYGFHNEQSASYAAGAVGYLTGRPGVCLAVSGPGMIHGIAGLANAWSNNWPMILIGGANDSYQNGQGAFQEAPQIESARPYVKYAARPDSIARLPFYVEQAVRTTIYGRPGAAYLDLPGDIISGSVEEAEVTYPGRCPEPPRTLAPEENIKAALAALKTAERPLVIVGKGAAYSRAEDEVRKFVETTGLPYLASPMGKGVIPDDHPQSIAAARSFALQNTDLVVLMGARMNWMMHFGQPPRWNEKVRVIQMDISAEEIGTNVPTEVALVGDAKAITAQLNAELEKNPWSYPSETTWWTGLQSKIAANAATVEPMFNDDSVPMGYYRVLRDIRDLIPKDAIISNEGASTMDIGRTVLPNFFARTRLDAATFGTMGVGAGQAIAAASVHPDRKIICVQGDSAFGFGGMEVETAARYGLNITFVIINNNGIGGGPDELDPAHIPPGAYTPQAHYEKMADVYGGKGYFVTTPDQLKPVLEEAMAQPKPAIVNIMISNKSGRKPQEFGWLTR

来源 Source

来源生物 organism	Thermoflexaceae bacterium
NCBI 分类编号 ncbi_taxonomy_id	2739507
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	THIAMINE DIPHOSPHATE
分子量 formula_weight	425.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	2

Entity 4 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	2

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	8

Entity 7 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 8 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	513

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7. 引用文献 (1)

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晶胞边长 a length_a	100.173 Å
晶胞边长 b length_b	182.511 Å
晶胞边长 c length_c	123.920 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	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	orthorhombic

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	37.380 Å
R 因子 r_factor	0.1993
R_work r_work	0.1975
R_free r_free	0.2343

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