9jm9

NADP-dependent oxidoreductase complexed with NADP and substrate 3

Method: X-RAY DIFFRACTION D_max: 106.3 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	9jm9
沉积日期 deposition_date	2024-09-20
最后修订 last_revision	2025-06-18
结构标题 title	NADP-dependent oxidoreductase complexed with NADP and substrate 3
关键词 keywords	alcohol dehydrogenase, complex, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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	30.25 Å
回转半径 Rg (电子) rg_electron	29.81 Å
零角强度 I(0) i0	196824000.00
分子量 molecular_weight	74225.0 kDa
排除体积 excluded_volume	71453 Å³
包络体积 envelope_volume	119800 Å³
水化壳体积 shell_volume	34294 Å³
包络直径 envelope_diameter	113.3 Å
壳层 Rg shell_rg	35.99 Å
包络 Rg envelope_rg	30.11 Å
形状 Rg shape_rg	29.76 Å
总 Rg total_rg	30.27 Å
总原子数 total_atoms	5639
残基数 n_residues	708
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	106.3 Å
Rg (实空间) rg_real	30.40 Å
Rg 误差 (实空间) rg_real_error	0.88 Å
I(0) (实空间) i0_real	1.9680e+08
I(0) 误差 (实空间) i0_real_error	3.3890e+06
Rg (倒空间) rg_reciprocal	30.34 Å
I(0) (倒空间) i0_reciprocal	196800000.0000
解质量估计 total_estimate	0.8497
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	30.7 Å
偏度 Skewness skewness	0.485
峰度 Kurtosis kurtosis	-0.262
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	43420000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.742; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.840; Smooth: 0.975

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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	NADP-dependent oxidoreductase
分子量 formula_weight	38943.3 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	5639

LGSMKTERWVVREHVEGVPDAARIYEKVETELNTRLGEEQMLLKTLYVSVDPYLQGICLDTPIGDHMGADSIMQVLDAGPNAPFRPGDLVQGFGGWRTHLVSDGKPKLWQTGTFPMVFPAYRKLDLRHYDDALPLSTALGVMGGPGMTAWGTMTKFMQVRPGDTVVVSGASGMIGTLVGQMAKRAGARVVGTAGSAGKARYLSQLGFDAVIDYKLADDADKMREALREAAPDGVDKYFDSIGGSVTDAVFSMLNVGSQVAVCWQWATQVQRDYHGPRLLPYIMFPRATIRGIFSLEWFTEQNWSALHEELGGLVRRQELVAHETVQDGFEHIPAAYQTLFSASESNRGKVLVRV

来源 Source

来源生物 organism	Lysobacter enzymogenes
NCBI 分类编号 ncbi_taxonomy_id	69
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
分子量 formula_weight	743.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	;(1Z,3E,5E,7R,8S,10R,11R,12S,15S,16E,18E,25S)-11-ethyl-2-hydroxy-10-methyl-21,26-diazatetracyclo[23.2.1.07,15.08,12]octacosa-1,3,5,13,16,18-hexaene-20,27,28-trione ;
分子量 formula_weight	476.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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晶胞边长 a length_a	87.790 Å
晶胞边长 b length_b	87.790 Å
晶胞边长 c length_c	219.611 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 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	3.380 Å
最低分辨率 resolution_low	62.080 Å
R 因子 r_factor	0.2051
R_work r_work	0.2010
R_free r_free	0.2848

fit	/app/data/saxs_computation/jm/9jm9/9jm9.fit
pddf	/app/data/pr_computation/jm/9jm9/9jm9.pr.out
profile	/app/data/saxs_computation/jm/9jm9/9jm9.dat

NADP-dependent oxidoreductase complexed with NADP and substrate 3

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