1oc7

;D405N mutant of the CELLOBIOHYDROLASE CEL6A FROM HUMICOLA INSOLENS in complex with methyl-tetrathio-alpha-d-cellopentoside at 1.1 angstrom resolution ;

Method: X-RAY DIFFRACTION D_max: 60.7 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	1oc7
沉积日期 deposition_date	2003-02-06
结构标题 title	;D405N mutant of the CELLOBIOHYDROLASE CEL6A FROM HUMICOLA INSOLENS in complex with methyl-tetrathio-alpha-d-cellopentoside at 1.1 angstrom resolution ;
关键词 keywords	HYDROLASE, CELLULOSE DEGRADATION, CELLOBIOHYDROLASE, CELLULASE, GLYCOSIDE HYDROLASE FAMILY 6, PROCESSIVE MECHANISM; 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	20.28 Å
回转半径 Rg (电子) rg_electron	19.17 Å
零角强度 I(0) i0	29962000.00
分子量 molecular_weight	41668.0 kDa
排除体积 excluded_volume	51759 Å³
包络体积 envelope_volume	56814 Å³
水化壳体积 shell_volume	23767 Å³
包络直径 envelope_diameter	61.4 Å
壳层 Rg shell_rg	26.56 Å
包络 Rg envelope_rg	19.37 Å
形状 Rg shape_rg	19.15 Å
总 Rg total_rg	20.09 Å
总原子数 total_atoms	2937
残基数 n_residues	364
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	60.7 Å
Rg (实空间) rg_real	20.11 Å
Rg 误差 (实空间) rg_real_error	0.28 Å
I(0) (实空间) i0_real	2.9960e+07
I(0) 误差 (实空间) i0_real_error	3.2900e+05
Rg (倒空间) rg_reciprocal	20.14 Å
I(0) (倒空间) i0_reciprocal	29960000.0000
解质量估计 total_estimate	0.9022
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	26.9 Å
偏度 Skewness skewness	0.031
峰度 Kurtosis kurtosis	-0.514
角度范围 angular_range	— – 0.3900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8581000.0000
实空间数据点数 n_real_points	71
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.993

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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 (8)

Entity 1 polymer

描述 description	CELLOBIOHYDROLASE II
分子量 formula_weight	40181.7 kDa
EC 编号 ec_number	3.2.1.91
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	3619

APYNGNPFEGVQLWANNYYRSEVHTLAIPQITDPALRAAASAVAEVPSFQWLDRNVTVDTLLVQTLSEIREANQAGANPQYAAQIVVYDLPDRDCAAAASNGEWAIANNGVNNYKAYINRIREILISFSDVRTILVIEPDSLANMVTNMNVPKCSGAASTYRELTIYALKQLDLPHVAMYMDAGHAGWLGWPANIQPAAELFAKIYEDAGKPRAVRGLATNVANYNAWSVSSPPPYTSPNPNYDEKHYIEAFRPLLEARGFPAQFIVDQGRSGKQPTGQKEWGHWCNAIGTGFGMRPTANTGHQYVDAFVWVKPGGECNGTSDTTAARYDYHCGLEDALKPAPEAGQWFNEYFIQLLRNANPPF

来源 Source

来源生物 organism	HUMICOLA INSOLENS
NCBI 分类编号 ncbi_taxonomy_id	34413
宿主生物 host_organism	ASPERGILLUS ORYZAE

Entity 2 branched

描述 description	;beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl 4-thio-alpha-D-glucopyranoside ;
分子量 formula_weight	907.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	ACETATE ION
分子量 formula_weight	59.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	DIMETHYLFORMAMIDE
分子量 formula_weight	73.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 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	2

Entity 8 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	603

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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	d1oc7a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.6 — 7-stranded beta/alpha barrel
超家族 Superfamily superfamily	c.6.1 — Glycosyl hydrolases family 6, cellulases
家族 Family family	c.6.1.1 — Glycosyl hydrolases family 6, cellulases

CATH v4.4 (1 domains)

结构域编号 domain_id	1oc7A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	40 — 1, 4-beta cellobiohydrolase

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7. 引用文献 (1)

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晶胞边长 a length_a	57.504 Å
晶胞边长 b length_b	60.148 Å
晶胞边长 c length_c	97.207 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	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.110 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1060
R_work r_work	0.1050
R_free r_free	0.1240

fit	/app/data/saxs_computation/oc/1oc7/1oc7.fit
pddf	/app/data/pr_computation/oc/1oc7/1oc7.pr.out
profile	/app/data/saxs_computation/oc/1oc7/1oc7.dat