SAXSdb — 2cn3

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2cn3
沉积日期 deposition_date	2006-05-17
结构标题 title	Crystal Structures of Clostridium thermocellum Xyloglucanase
关键词 keywords	GLYCOSYLHYDROLASE, HYDROLASE, FAMILY GH74, XYLOGLUCANASE; 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	45.07 Å
回转半径 Rg (电子) rg_electron	45.59 Å
零角强度 I(0) i0	397913000.00
分子量 molecular_weight	164990.0 kDa
排除体积 excluded_volume	206130 Å³
包络体积 envelope_volume	256690 Å³
水化壳体积 shell_volume	49609 Å³
包络直径 envelope_diameter	156.3 Å
壳层 Rg shell_rg	46.24 Å
包络 Rg envelope_rg	45.29 Å
形状 Rg shape_rg	45.60 Å
总 Rg total_rg	45.60 Å
总原子数 total_atoms	11637
残基数 n_residues	1456
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	145.5 Å
Rg (实空间) rg_real	45.60 Å
Rg 误差 (实空间) rg_real_error	1.31 Å
I(0) (实空间) i0_real	3.9790e+08
I(0) 误差 (实空间) i0_real_error	6.7150e+06
Rg (倒空间) rg_reciprocal	45.08 Å
I(0) (倒空间) i0_reciprocal	397700000.0000
解质量估计 total_estimate	0.7573
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	33.2 Å
偏度 Skewness skewness	0.500
峰度 Kurtosis kurtosis	-0.608
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	128500000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.702; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.598; Smooth: 0.138

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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 (5)

Entity 1 polymer

描述 description	BETA-1,4-XYLOGLUCAN HYDROLASE
分子量 formula_weight	80961.6 kDa
EC 编号 ec_number	3.2.1.151
突变 mutation	YES
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	12865

ISSQAVTSVPYKWDNVVIGGGGGFMPGIVFNETEKDLIYARAAIGGAYRWDPSTETWIPLLDHFQMDEYSYYGVESIATDPVDPNRVYIVAGMYTNDWLPNMGAILRSTDRGETWEKTILPFKMGGNMPGRSMGERLAIDPNDNRILYLGTRCGNGLWRSTDYGVTWSKVESFPNPGTYIYDPNFDYTKDIIGVVWVVFDKSSSTPGNPTKTIYVGVADKNESIYRSTDGGVTWKAVPGQPKGLLPHHGVLASNGMLYITYGDTCGPYDGNGKGQVWKFNTRTGEWIDITPIPYSSSDNRFCFAGLAVDRQNPDIIMVTSMNAWWPDEYIFRSTDGGATWKNIWEWGMYPERILHYEIDISAAPWLDWGTEKQLPEINPKLGWMIGDIEIDPFNSDRMMYVTGATIYGCDNLTDWDRGGKVKIEVKATGIEECAVLDLVSPPEGAPLVSAVGDLVGFVHDDLKVGPKKMHVPSYSSGTGIDYAELVPNFMALVAKADLYDVKKISFSYDGGRNWFQPPNEAPNSVGGGSVAVAADAKSVIWTPENASPAVTTDNGNSWKVCTNLGMGAVVASDRVNGKKFYAFYNGKFYISTDGGLTFTDTKAPQLPKSVNKIKAVPGKEGHVWLAAREGGLWRSTDGGYTFEKLSNVDTAHVVGFGKAAPGQDYMAIYITGKIDNVLGFFRSDDAGKTWVRINDDEHGYGAVDTAITGDPRVYGRVYIATNGRGIVYGEPASDEPV

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	;alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose ;
分子量 formula_weight	1225.1 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 3 branched

描述 description	;alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose ;
分子量 formula_weight	1387.2 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	2

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	1228

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2cn3a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.13 — Oligoxyloglucan reducing end-specific cellobiohydrolase
家族 Family family	b.69.13.0 — automated matches

结构域编号 domain_id	d2cn3a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.13 — Oligoxyloglucan reducing end-specific cellobiohydrolase
家族 Family family	b.69.13.0 — automated matches

结构域编号 domain_id	d2cn3b1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.13 — Oligoxyloglucan reducing end-specific cellobiohydrolase
家族 Family family	b.69.13.0 — automated matches

结构域编号 domain_id	d2cn3b2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.13 — Oligoxyloglucan reducing end-specific cellobiohydrolase
家族 Family family	b.69.13.0 — automated matches

CATH v4.4 (4 domains)

结构域编号 domain_id	2cn3A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	2cn3A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	2cn3B01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	2cn3B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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7. 引用文献 (1)

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晶胞边长 a length_a	141.440 Å
晶胞边长 b length_b	141.440 Å
晶胞边长 c length_c	193.393 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	16

空间群 space_group	P 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	1.950 Å
最低分辨率 resolution_low	19.960 Å
R 因子 r_factor	0.1800
R_work r_work	0.1780
R_free r_free	0.2040

fit	/app/data/saxs_computation/cn/2cn3/2cn3.fit
pddf	/app/data/pr_computation/cn/2cn3/2cn3.pr.out
profile	/app/data/saxs_computation/cn/2cn3/2cn3.dat

Crystal Structures of Clostridium thermocellum Xyloglucanase

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