9gcj

;The crystal structure of beta-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus in complex with beta-D-glucose determined at 1.95 A resolution ;

Method: X-RAY DIFFRACTION D_max: 118.6 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	9gcj
沉积日期 deposition_date	2024-08-01
最后修订 last_revision	2024-10-16
结构标题 title	;The crystal structure of beta-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus in complex with beta-D-glucose determined at 1.95 A resolution ;
关键词 keywords	Biocatalysis, beta-glucosidase, Caldicellulosiruptor saccharolyticus, 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	34.98 Å
回转半径 Rg (电子) rg_electron	34.85 Å
零角强度 I(0) i0	163443000.00
分子量 molecular_weight	108000.0 kDa
排除体积 excluded_volume	136760 Å³
包络体积 envelope_volume	164560 Å³
水化壳体积 shell_volume	40031 Å³
包络直径 envelope_diameter	126.2 Å
壳层 Rg shell_rg	40.40 Å
包络 Rg envelope_rg	35.06 Å
形状 Rg shape_rg	34.81 Å
总 Rg total_rg	35.39 Å
总原子数 total_atoms	15103
残基数 n_residues	911
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	118.6 Å
Rg (实空间) rg_real	35.19 Å
Rg 误差 (实空间) rg_real_error	1.08 Å
I(0) (实空间) i0_real	1.6340e+08
I(0) 误差 (实空间) i0_real_error	2.6010e+06
Rg (倒空间) rg_reciprocal	35.06 Å
I(0) (倒空间) i0_reciprocal	163400000.0000
解质量估计 total_estimate	0.8376
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	31.6 Å
偏度 Skewness skewness	0.462
峰度 Kurtosis kurtosis	-0.535
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	58630000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.700; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.860; Smooth: 0.925

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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 (6)

Entity 1 polymer

描述 description	beta-glucosidase
分子量 formula_weight	54175.4 kDa
EC 编号 ec_number	3.2.1.21
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	15517

GSHMLEDPMSFPKGFLWGAATASYQIEGAWNEDGKGESIWDRFTHQKRNILYGHNGDVACDHYHRFEEDVSLMKELGLKAYRFSIAWTRIFPDGFGTVNQKGLEFYDRLINKLVENGIEPVVTLYHWDLPQKLQDIGGWANPEIVNYYFDYAMLVINRYKDKVKKWITFNEPYCIAFLGYFHGIHAPGIKDFKVAMDVVHSLMLSHFKVVKAVKENNIDVEVGITLNLTPVYLQTERLGYKVSEIEREMVSLSSQLDNQLFLDPVLKGSYPQKLLDYLVQKDLLDSQKALSMQQEVKENFIFPDFLGINYYTRAVRLYDENSSWIFPIRWEHPAGEYTEMGWEVFPQGLFDLLIWIKESYPQIPIYITENGAAYNDIVTEDGKVHDSKRIEYLKQHFEAARKAIENGVDLRGYFVWSLMDNFEWAMGYTKRFGIIYVDYETQKRIKKDSFYFYQQYIKENS

来源 Source

来源生物 organism	Caldicellulosiruptor saccharolyticus DSM 8903
NCBI 分类编号 ncbi_taxonomy_id	351627
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

描述 description	beta-D-glucopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	PENTAETHYLENE GLYCOL
分子量 formula_weight	238.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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 5 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 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	402

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7. 引用文献 (1)

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晶胞边长 a length_a	68.161 Å
晶胞边长 b length_b	98.307 Å
晶胞边长 c length_c	81.776 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.63 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.950 Å
最低分辨率 resolution_low	62.615 Å
R 因子 r_factor	—
R_work r_work	0.1713
R_free r_free	0.2072

fit	/app/data/saxs_computation/gc/9gcj/9gcj.fit
pddf	/app/data/pr_computation/gc/9gcj/9gcj.pr.out
profile	/app/data/saxs_computation/gc/9gcj/9gcj.dat