SAXSdb — 1f9d

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1f9d
沉积日期 deposition_date	2000-07-10
结构标题 title	Crystal structure of the cellulase CEL48F from C. cellulolyticum in complex with cellotetraose
关键词 keywords	Cellulase, Protein-Cellotetraose Complex, HYDROLASE; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	24.33 Å
回转半径 Rg (电子) rg_electron	23.10 Å
零角强度 I(0) i0	86593000.00
分子量 molecular_weight	72334.0 kDa
排除体积 excluded_volume	89716 Å³
包络体积 envelope_volume	99272 Å³
水化壳体积 shell_volume	33727 Å³
包络直径 envelope_diameter	74.6 Å
壳层 Rg shell_rg	31.89 Å
包络 Rg envelope_rg	23.35 Å
形状 Rg shape_rg	23.08 Å
总 Rg total_rg	24.03 Å
总原子数 total_atoms	5117
残基数 n_residues	629
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	74.7 Å
Rg (实空间) rg_real	24.12 Å
Rg 误差 (实空间) rg_real_error	0.26 Å
I(0) (实空间) i0_real	8.6590e+07
I(0) 误差 (实空间) i0_real_error	9.8500e+05
Rg (倒空间) rg_reciprocal	24.17 Å
I(0) (倒空间) i0_reciprocal	86600000.0000
解质量估计 total_estimate	0.8996
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	73.5 Å
偏度 Skewness skewness	0.084
峰度 Kurtosis kurtosis	-0.528
角度范围 angular_range	— – 0.3250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	35130000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.995

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	ENDO-1,4-BETA-GLUCANASE F
分子量 formula_weight	70868.9 kDa
EC 编号 ec_number	3.2.1.4
突变 mutation	E55Q
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	5340

ASSPANKVYQDRFESMYSKIKDPANGYFSEQGIPYHSIETLMVEAPDYGHVTTSQAMSYYMWLEAMHGRFSGDFTGFDKSWSVTEQYLIPTEKDQPNTSMSRYDANKPATYAPEFQDPSKYPSPLDTSQPVGRDPINSQLTSAYGTSMLYGMHWILDVDNWYGFGARADGTSKPSYINTFQRGEQESTWETIPQPCWDEHKFGGQYGFLDLFTKDTGTPAKQFKYTNAPDADARAVQATYWADQWAKEQGKSVSTSVGKATKMGDYLRYSFFDKYFRKIGQPSQAGTGYDAAHYLLSWYYAWGGGIDSTWSWIIGSSHNHFGYQNPFAAWVLSTDANFKPKSSNGASDWAKSLDRQLEFYQWLQSAEGAIAGGATNSWNGRYEAVPSGTSTFYGMGYVENPVYADPGSNTWFGMQVWSMQRVAELYYKTGDARAKKLLDKWAKWINGEIKFNADGTFQIPSTIDWEGQPDTWNPTQGYTGNANLHVKVVNYGTDLGCASSLANTLTYYAAKSGDETSRQNAQKLLDAMWNNYSDSKGISTVEQRGDYHRFLDQEVFVPAGWTGKMPNGDVIKSGVKFIDIRSKYKQDPEWQTMVAALQAGQVPTQRLHRFWAQSEFAVANGVYAILFPD

来源 Source

来源生物 organism	Clostridium cellulolyticum
NCBI 分类编号 ncbi_taxonomy_id	1521
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	;alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ;
分子量 formula_weight	828.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
分子量 formula_weight	666.6 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	223

▼

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1f9da_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.102 — alpha/alpha toroid
超家族 Superfamily superfamily	a.102.1 — Six-hairpin glycosidases
家族 Family family	a.102.1.2 — Cellulases catalytic domain

CATH v4.4 (3 domains)

结构域编号 domain_id	1f9dA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	50 — Alpha/alpha barrel
拓扑 Topology topology	10 — Glycosyltransferase
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1f9dA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	160 — Endo-1,4-beta-glucanase f; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Endo-1,4-beta-glucanase f. Domain 2

结构域编号 domain_id	1f9dA03
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	870 — Endo-1,4-beta-glucanase f; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Endo-1,4-beta-glucanase f. Domain 3

▶

7. 引用文献 (2)

▶

晶胞边长 a length_a	61.330 Å
晶胞边长 b length_b	84.740 Å
晶胞边长 c length_c	121.720 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	2.300 Å
最低分辨率 resolution_low	54.800 Å
R 因子 r_factor	—
R_work r_work	0.1510
R_free r_free	0.1890

fit	/app/data/saxs_computation/f9/1f9d/1f9d.fit
pddf	/app/data/pr_computation/f9/1f9d/1f9d.pr.out
profile	/app/data/saxs_computation/f9/1f9d/1f9d.dat

Crystal structure of the cellulase CEL48F from C. cellulolyticum in complex with cellotetraose

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