8uy1

Methylenetetrahydrofolate reductase from Chaetomium thermophilum DSM 1495, Active (R) State

Method: X-RAY DIFFRACTION D_max: 156.2 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	8uy1
沉积日期 deposition_date	2023-11-12
结构标题 title	Methylenetetrahydrofolate reductase from Chaetomium thermophilum DSM 1495, Active (R) State
关键词 keywords	;methylenetetrahydrofolate reductase, NADPH activity, oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor cobalamin binding, one-carbon metabolism, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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	47.27 Å
回转半径 Rg (电子) rg_electron	46.92 Å
零角强度 I(0) i0	1124450000.00
分子量 molecular_weight	273910.0 kDa
排除体积 excluded_volume	340840 Å³
包络体积 envelope_volume	460580 Å³
水化壳体积 shell_volume	82425 Å³
包络直径 envelope_diameter	164.4 Å
壳层 Rg shell_rg	50.49 Å
包络 Rg envelope_rg	46.24 Å
形状 Rg shape_rg	46.84 Å
总 Rg total_rg	47.31 Å
总原子数 total_atoms	19293
残基数 n_residues	2362
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	156.2 Å
Rg (实空间) rg_real	47.16 Å
Rg 误差 (实空间) rg_real_error	1.21 Å
I(0) (实空间) i0_real	1.1240e+09
I(0) 误差 (实空间) i0_real_error	1.9680e+07
Rg (倒空间) rg_reciprocal	47.27 Å
I(0) (倒空间) i0_reciprocal	1125000000.0000
解质量估计 total_estimate	0.8817
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	56.8 Å
偏度 Skewness skewness	0.266
峰度 Kurtosis kurtosis	-0.379
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	83320000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.845

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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 (3)

Entity 1 polymer

描述 description	Methylenetetrahydrofolate reductase-like protein
分子量 formula_weight	70407.7 kDa
突变 mutation	E21Q,L393M,V516F
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	D,A,B,C
原子数 atom_count	19297

SNAMHIRDMLAEAERTGEPSFSFQYFPPKTAQGVQNLYDRMERMYNYGPKFIDITWGAGGRVAELTCEMVVQAQAYLGLETCMHLTCTDMGVERINDALRKAYKAGCTNILALRGDPPRDKEKWEAAKDGFRYAKDLVAHIRKEYGDHFDIGVAGYPEGCDDNKDEDLLLDHLKEKVDMGAGFIVTQMFYDVDNFLRWVKKVRERGISVPIVPGIMPIATYASFLRRANHMKCKIPEEWMAKLEPVKNDDVAVREIGKTLVADMCRKILDAGIRHLHFYTMNLAQATRMVLEELNWLPSPDRPLKHALPWKQSLGFGRRGEDVRPIFWRNRNKSYVARTQDWDEFPNGRWGDSRSPAFGELDAYGVGLTGSNEQNRERWGEPKCIRDIANLFIRYMRKEIDYLPWSEAPVADEADLIKDELIDLNRRGLITVNSQPAVNGAKSNHPVHGWGPSNGYVYQKAYLEFFVSPELYPEIKRRIESHPDLTYHAVTKSGNLETNAQSDGPNAVTWGVFPGKEIFQPTIVERISFLAWKDEAYHLGMEWARCYDAGSPSRVLLEEMMNTWWLVNIVNNDFHQGNTLFEILKGLEVTDLDKVPETQANGTNGVSNGVKASETSV

来源 Source

来源生物 organism	Thermochaetoides thermophila DSM 1495
NCBI 分类编号 ncbi_taxonomy_id	759272
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 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	4

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7. 引用文献 (1)

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晶胞边长 a length_a	117.972 Å
晶胞边长 b length_b	151.380 Å
晶胞边长 c length_c	188.048 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	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	3.490 Å
最低分辨率 resolution_low	52.040 Å
R 因子 r_factor	0.2176
R_work r_work	0.2156
R_free r_free	0.2556

fit	/app/data/saxs_computation/uy/8uy1/8uy1.fit
pddf	/app/data/pr_computation/uy/8uy1/8uy1.pr.out
profile	/app/data/saxs_computation/uy/8uy1/8uy1.dat

Methylenetetrahydrofolate reductase from Chaetomium thermophilum DSM 1495, Active (R) State

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction