9gmj

;The crystal structure of ManDH5 Selenomethionine derivative at 1.6 Angstroms resolution - a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium ;

Method: X-RAY DIFFRACTION D_max: 89.8 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	9gmj
沉积日期 deposition_date	2024-08-28
最后修订 last_revision	2025-09-10
结构标题 title	;The crystal structure of ManDH5 Selenomethionine derivative at 1.6 Angstroms resolution - a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium ;
关键词 keywords	Glycoside-Hydrolase, Mannanase, Thermostable protein, HYDROLASE; HYDROLASE
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	26.06 Å
回转半径 Rg (电子) rg_electron	25.37 Å
零角强度 I(0) i0	65021000.00
分子量 molecular_weight	66676.0 kDa
排除体积 excluded_volume	84571 Å³
包络体积 envelope_volume	96588 Å³
水化壳体积 shell_volume	31512 Å³
包络直径 envelope_diameter	92.4 Å
壳层 Rg shell_rg	33.09 Å
包络 Rg envelope_rg	25.91 Å
形状 Rg shape_rg	25.34 Å
总 Rg total_rg	26.27 Å
总原子数 total_atoms	4722
残基数 n_residues	556
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	89.8 Å
Rg (实空间) rg_real	26.08 Å
Rg 误差 (实空间) rg_real_error	0.62 Å
I(0) (实空间) i0_real	6.5020e+07
I(0) 误差 (实空间) i0_real_error	9.0010e+05
Rg (倒空间) rg_reciprocal	26.07 Å
I(0) (倒空间) i0_reciprocal	65020000.0000
解质量估计 total_estimate	0.6780
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	30.9 Å
偏度 Skewness skewness	0.448
峰度 Kurtosis kurtosis	-0.083
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	23940000.0000
实空间数据点数 n_real_points	62
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.747; Stabil: 1.000; Sysdev: 0.221; Positv: 1.000; Valcen: 0.980; Smooth: 0.929

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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	DUF5060 domain-containing protein
分子量 formula_weight	67689.8 kDa
突变 mutation	;Selenomethionine replacing all Metionine residues; According to the phase solution (performed using Crank 2), only 6 out of 7 MET residues were substituted by MSE. The first in the sequence appears to be MET. ;
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	5168

ESRYKDNRPLNILGIDISKMELGRYNLFEVSIFLQGSYLNPFDPQEIDVEGIFEDQYGNQYRVPGFFYQEYKRELKNDYEYLVPVGDPYFKIRFSPINIGSYKFFIKVKDKTGREVSSDKYTIYVKESEKPGYIRVSEKNWRYFKFDNGRQFLPIGANICWATSKGTYDYDVWLPKCAENGGNYFRVWLGPSWATFALERESVKEYDLKNAWKLDYVLNLAEKLNMYIMFCFDSYNELRYQKEGAYPYWEHTPHYEKNGGPLKEPKDFWTNNEMIKYYKNKLRYIVARYGYSTNVFAWEFWNEVDIISPTAFVIGEVKKWHEDMAKYLNSIDPWKHLITTSFAFSPGKPEIDSISGLNFVQTHIYKSNRYIDALLSLIAYKEKYRKPHLVGEFGLDAGGNDLWVDPNGYVIHNAIWTTILSGASGTAMSWWWDNHIHPNNLYFHYRALADFVKDINFLEEKFERLTNYKFNVYNREIKVIGLQGKKYILLWLYNAKEAYQYKKDIPNMDSSKFLGSIELLIKPPIKVIYYDTYRGEKIKELDLDKNVIPIIEFERDLAIKIELLGEGE

来源 Source

来源生物 organism	Dictyoglomus thermophilum
NCBI 分类编号 ncbi_taxonomy_id	14
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
分子量 formula_weight	122.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	420

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7. 引用文献 (1)

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晶胞边长 a length_a	95.207 Å
晶胞边长 b length_b	99.274 Å
晶胞边长 c length_c	153.724 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	8

空间群 space_group	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	orthorhombic

分辨率 resolution	1.600 Å
最低分辨率 resolution_low	83.400 Å
R 因子 r_factor	0.1776
R_work r_work	0.1770
R_free r_free	0.1903

fit	/app/data/saxs_computation/gm/9gmj/9gmj.fit
pddf	/app/data/pr_computation/gm/9gmj/9gmj.pr.out
profile	/app/data/saxs_computation/gm/9gmj/9gmj.dat

;The crystal structure of ManDH5 Selenomethionine derivative at 1.6 Angstroms resolution - a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium ;

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