1l1y

;The Crystal Structure and Catalytic Mechanism of Cellobiohydrolase CelS, the Major Enzymatic Component of the Clostridium thermocellum cellulosome ;

Method: X-RAY DIFFRACTION D_max: 156.9 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	1l1y
沉积日期 deposition_date	2002-02-20
结构标题 title	;The Crystal Structure and Catalytic Mechanism of Cellobiohydrolase CelS, the Major Enzymatic Component of the Clostridium thermocellum cellulosome ;
关键词 keywords	alpha/alpha barrel, 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	49.38 Å
回转半径 Rg (电子) rg_electron	48.79 Å
零角强度 I(0) i0	2691770000.00
分子量 molecular_weight	435340.0 kDa
排除体积 excluded_volume	542280 Å³
包络体积 envelope_volume	677430 Å³
水化壳体积 shell_volume	110050 Å³
包络直径 envelope_diameter	159.0 Å
壳层 Rg shell_rg	56.83 Å
包络 Rg envelope_rg	48.09 Å
形状 Rg shape_rg	48.80 Å
总 Rg total_rg	48.97 Å
总原子数 total_atoms	30862
残基数 n_residues	3852
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	156.9 Å
Rg (实空间) rg_real	48.98 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	2.6920e+09
I(0) 误差 (实空间) i0_real_error	4.5470e+07
Rg (倒空间) rg_reciprocal	49.38 Å
I(0) (倒空间) i0_reciprocal	2693000000.0000
解质量估计 total_estimate	0.8837
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	68.7 Å
偏度 Skewness skewness	0.070
峰度 Kurtosis kurtosis	-0.500
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	858000000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.911

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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 (3)

Entity 1 polymer

描述 description	cellobiohydrolase
分子量 formula_weight	76638.3 kDa
EC 编号 ec_number	3.2.1.4
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	32457

MVKSRKISILLAVAMLVSIMIPTTAFAGPTKAPTKDGTSYKDLFLELYGKIKDPKNGYFSPDEGIPYHSIETLIVEAPDYGHVTTSEAFSYYVWLEAMYGNLTGNWSGVETAWKVMEDWIIPDSTEQPGMSSYNPNSPATYADEYEDPSYYPSELKFDTVRVGSDPVHNDLVSAYGPNMYLMHWLMDVDNWYGFGTGTRATFINTFQRGEQESTWETIPHPSIEEFKYGGPNGFLDLFTKDRSYAKQWRYTNAPDAEGRAIQAVYWANKWAKEQGKGSAVASVVSKAAKMGDFLRNDMFDKYFMKIGAQDKTPATGYDSAHYLMAWYTAWGGGIGASWAWKIGCSHAHFGYQNPFQGWVSATQSDFAPKSSNGKRDWTTSYKRQLEFYQWLQSAEGGIAGGATNSWNGRYEKYPAGTSTFYGMAYVPHPVYADPGSNQWFGFQAWSMQRVMEYYLETGDSSVKNLIKKWVDWVMSEIKLYDDGTFAIPSDLEWSGQPDTWTGTYTGNPNLHVRVTSYGTDLGVAGSLANALATYAAATERWEGKLDTKARDMAAELVNRAWYNFYCSEGKGVVTEEARADYKRFFEQEVYVPAGWSGTMPNGDKIQPGIKFIDIRTKYRQDPYYDIVYQAYLRGEAPVLNYHRFWHEVDLAVAMGVLATYFPDMTYKVPGTPSTKLYG

来源 Source

来源生物 organism	Clostridium thermocellum
NCBI 分类编号 ncbi_taxonomy_id	1515
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	beta-D-glucopyranose-(1-4)-beta-D-glucopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	man
拷贝数 entity_count	6

Entity 3 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	1595

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1l1ya_
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

结构域编号 domain_id	d1l1yb_
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

结构域编号 domain_id	d1l1yc_
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

结构域编号 domain_id	d1l1yd_
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

结构域编号 domain_id	d1l1ye_
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

结构域编号 domain_id	d1l1yf_
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 (18 domains)

结构域编号 domain_id	1l1yA01
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	1l1yA02
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	1l1yA03
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

结构域编号 domain_id	1l1yB01
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	1l1yB02
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	1l1yB03
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

结构域编号 domain_id	1l1yC01
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	1l1yC02
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	1l1yC03
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

结构域编号 domain_id	1l1yD01
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	1l1yD02
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	1l1yD03
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

结构域编号 domain_id	1l1yE01
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	1l1yE02
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	1l1yE03
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

结构域编号 domain_id	1l1yF01
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	1l1yF02
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	1l1yF03
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

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7. 引用文献 (1)

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晶胞边长 a length_a	147.243 Å
晶胞边长 b length_b	207.204 Å
晶胞边长 c length_c	213.220 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	24

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	2.400 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.1908
R_work r_work	0.1890
R_free r_free	0.2244

fit	/app/data/saxs_computation/l1/1l1y/1l1y.fit
pddf	/app/data/pr_computation/l1/1l1y/1l1y.pr.out
profile	/app/data/saxs_computation/l1/1l1y/1l1y.dat