2jen

Family 12 xyloglucanase from Bacillus licheniformis in complex with ligand

Method: X-RAY DIFFRACTION D_max: 53.0 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	2jen
沉积日期 deposition_date	2007-01-18
结构标题 title	Family 12 xyloglucanase from Bacillus licheniformis in complex with ligand
关键词 keywords	PLANT CELL WALL, GLYCOSIDASE, XYLOGLUCANASE, HYDROLASE, FAMILY 12; 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	17.98 Å
回转半径 Rg (电子) rg_electron	16.51 Å
零角强度 I(0) i0	14307500.00
分子量 molecular_weight	27982.0 kDa
排除体积 excluded_volume	34651 Å³
包络体积 envelope_volume	37480 Å³
水化壳体积 shell_volume	18374 Å³
包络直径 envelope_diameter	52.4 Å
壳层 Rg shell_rg	23.26 Å
包络 Rg envelope_rg	16.79 Å
形状 Rg shape_rg	16.46 Å
总 Rg total_rg	17.63 Å
总原子数 total_atoms	1978
残基数 n_residues	233
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	53.0 Å
Rg (实空间) rg_real	17.80 Å
Rg 误差 (实空间) rg_real_error	0.17 Å
I(0) (实空间) i0_real	1.4310e+07
I(0) 误差 (实空间) i0_real_error	1.4620e+05
Rg (倒空间) rg_reciprocal	17.82 Å
I(0) (倒空间) i0_reciprocal	14310000.0000
解质量估计 total_estimate	0.9043
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	23.6 Å
偏度 Skewness skewness	0.043
峰度 Kurtosis kurtosis	-0.494
角度范围 angular_range	— – 0.4400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4386000.0000
实空间数据点数 n_real_points	75
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.977

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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 (7)

Entity 1 polymer

描述 description	ENDO-BETA-1,4-GLUCANASE
分子量 formula_weight	29035.2 kDa
EC 编号 ec_number	3.2.1.4, 3.2.1.151
突变 mutation	YES
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	2483

MKNNHLLKSILLWGAVCIIVLAGPLSAFAASSSNPSDKLYFKNKKYYIFNNVWGADQVSGWWQTIYHNSDSDMGWVWNWPSNTSTVKAYPSIVSGWHWTEGYTAGSGFPTRLSDQKNINTKVSYSISANGTYNAAYDIWLHNTNKASWDSAPTDAIMIWLNNTNAGPAGSYVETVSIGGHSWKVYKGYIDAGGGKGWNVFSFIRTANTQSANLNIRDFTNYLADSKQWLSKTKYVSSVEFGTEVFGGTGQINISNWDVTVR

来源 Source

来源生物 organism	BACILLUS LICHENIFORMIS
NCBI 分类编号 ncbi_taxonomy_id	1402
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 branched

描述 description	;beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ;
分子量 formula_weight	930.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	alpha-D-xylopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]alpha-D-glucopyranose
分子量 formula_weight	606.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	1,4-DIETHYLENE DIOXIDE
分子量 formula_weight	88.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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 6 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 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	361

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d2jena_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.29 — Concanavalin A-like lectins/glucanases
超家族 Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
家族 Family family	b.29.1.0 — automated matches

CATH v4.4 (1 domains)

结构域编号 domain_id	2jenA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	180 — Glycoside hydrolase family 11/12, catalytic domain

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7. 引用文献 (1)

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晶胞边长 a length_a	114.629 Å
晶胞边长 b length_b	114.629 Å
晶胞边长 c length_c	110.302 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	120.00 °
晶胞分子数 Z z_pdb	18

空间群 space_group	H 3 2
空间群编号 int_tables_number	155
晶系 crystal_system	—

分辨率 resolution	1.400 Å
最低分辨率 resolution_low	74.540 Å
R 因子 r_factor	0.1160
R_work r_work	0.1150
R_free r_free	0.1410

fit	/app/data/saxs_computation/je/2jen/2jen.fit
pddf	/app/data/pr_computation/je/2jen/2jen.pr.out
profile	/app/data/saxs_computation/je/2jen/2jen.dat