9d7l

Minimal PutA proline dehydrogenase domain (design #2) covalently inactivated by (S)-but-3-yn-2-ylglycine

Method: X-RAY DIFFRACTION D_max: 89.0 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	9d7l
沉积日期 deposition_date	2024-08-16
结构标题 title	Minimal PutA proline dehydrogenase domain (design #2) covalently inactivated by (S)-but-3-yn-2-ylglycine
关键词 keywords	BETA/ALPHA BARREL, FLAVOENZYME, PROLINE CATABOLISM, 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	28.48 Å
回转半径 Rg (电子) rg_electron	27.85 Å
零角强度 I(0) i0	199434000.00
分子量 molecular_weight	74334.0 kDa
排除体积 excluded_volume	71548 Å³
包络体积 envelope_volume	118620 Å³
水化壳体积 shell_volume	35155 Å³
包络直径 envelope_diameter	86.5 Å
壳层 Rg shell_rg	35.50 Å
包络 Rg envelope_rg	27.53 Å
形状 Rg shape_rg	27.84 Å
总 Rg total_rg	28.39 Å
总原子数 total_atoms	5630
残基数 n_residues	764
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	89.0 Å
Rg (实空间) rg_real	28.43 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	1.9940e+08
I(0) 误差 (实空间) i0_real_error	2.9010e+06
Rg (倒空间) rg_reciprocal	28.45 Å
I(0) (倒空间) i0_reciprocal	199400000.0000
解质量估计 total_estimate	0.9048
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	30.2 Å
偏度 Skewness skewness	0.269
峰度 Kurtosis kurtosis	-0.612
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	47760000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.952

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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	Bifunctional protein PutA
分子量 formula_weight	43774.0 kDa
EC 编号 ec_number	1.5.5.2,1.2.1.88
突变 mutation	residues 84-189 replaced by SSGS
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	5900

SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGSSGSMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRINDPKVSIDELIADPVEVVR

来源 Source

来源生物 organism	Sinorhizobium meliloti
NCBI 分类编号 ncbi_taxonomy_id	707241
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	;{[(3E)-4-{10-[(2S,3S,4R)-5-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-2,3,4-trihydroxypentyl]-7,8-dimethyl-2,4-dioxo-2,3,4,10-tetrahydrobenzo[g]pteridin-5(1H)-yl}but-3-en-2-ylidene]amino}acetic acid (non-preferred name) ;
分子量 formula_weight	912.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	FORMIC ACID
分子量 formula_weight	46.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	258

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7. 引用文献 (1)

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晶胞边长 a length_a	48.528 Å
晶胞边长 b length_b	54.242 Å
晶胞边长 c length_c	75.600 Å
晶胞夹角 α angle_alpha	103.96 °
晶胞夹角 β angle_beta	100.27 °
晶胞夹角 γ angle_gamma	109.32 °
晶胞分子数 Z z_pdb	2

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

分辨率 resolution	1.680 Å
最低分辨率 resolution_low	48.440 Å
R 因子 r_factor	0.2006
R_work r_work	0.1993
R_free r_free	0.2264

fit	/app/data/saxs_computation/d7/9d7l/9d7l.fit
pddf	/app/data/pr_computation/d7/9d7l/9d7l.pr.out
profile	/app/data/saxs_computation/d7/9d7l/9d7l.dat

Minimal PutA proline dehydrogenase domain (design #2) covalently inactivated by (S)-but-3-yn-2-ylglycine

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