2cn2

Crystal Structures of Clostridium thermocellum Xyloglucanase

Method: X-RAY DIFFRACTION D_max: 149.7 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	2cn2
沉积日期 deposition_date	2006-05-17
结构标题 title	Crystal Structures of Clostridium thermocellum Xyloglucanase
关键词 keywords	HYDROLASE, GH74 FAMILY, XYLOGLUCANASE, GLYCOSYLHYDROLASE; 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	45.71 Å
回转半径 Rg (电子) rg_electron	45.44 Å
零角强度 I(0) i0	1478820000.00
分子量 molecular_weight	313360.0 kDa
排除体积 excluded_volume	387250 Å³
包络体积 envelope_volume	492840 Å³
水化壳体积 shell_volume	88682 Å³
包络直径 envelope_diameter	152.3 Å
壳层 Rg shell_rg	51.30 Å
包络 Rg envelope_rg	44.75 Å
形状 Rg shape_rg	45.46 Å
总 Rg total_rg	45.59 Å
总原子数 total_atoms	21794
残基数 n_residues	2744
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	149.7 Å
Rg (实空间) rg_real	45.56 Å
Rg 误差 (实空间) rg_real_error	1.03 Å
I(0) (实空间) i0_real	1.4790e+09
I(0) 误差 (实空间) i0_real_error	2.5840e+07
Rg (倒空间) rg_reciprocal	45.71 Å
I(0) (倒空间) i0_reciprocal	1479000000.0000
解质量估计 total_estimate	0.8161
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	55.6 Å
偏度 Skewness skewness	0.241
峰度 Kurtosis kurtosis	-0.362
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	168800000.0000
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: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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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	BETA-1,4-XYLOGLUCAN HYDROLASE
分子量 formula_weight	81849.7 kDa
EC 编号 ec_number	3.2.1.151
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	23900

ISSQAVTSVPYKWDNVVIGGGGGFMPGIVFNETEKDLIYARADIGGAYRWDPSTETWIPLLDHFQMDEYSYYGVESIATDPVDPNRVYIVAGMYTNDWLPNMGAILRSTDRGETWEKTILPFKMGGNMPGRSMGERLAIDPNDNRILYLGTRCGNGLWRSTDYGVTWSKVESFPNPGTYIYDPNFDYTKDIIGVVWVVFDKSSSTPGNPTKTIYVGVADKNESIYRSTDGGVTWKAVPGQPKGLLPHHGVLASNGMLYITYGDTCGPYDGNGKGQVWKFNTRTGEWIDITPIPYSSSDNRFCFAGLAVDRQNPDIIMVTSMNAWWPDEYIFRSTDGGATWKNIWEWGMYPERILHYEIDISAAPWLDWGTEKQLPEINPKLGWMIGDIEIDPFNSDRMMYVTGATIYGCDNLTDWDRGGKVKIEVKATGIEECAVLDLVSPPEGAPLVSAVGDLVGFVHDDLKVGPKKMHVPSYSSGTGIDYAELVPNFMALVAKADLYDVKKISFSYDGGRNWFQPPNEAPNSVGGGSVAVAADAKSVIWTPENASPAVTTDNGNSWKVCTNLGMGAVVASDRVNGKKFYAFYNGKFYISTDGGLTFTDTKAPQLPKSVNKIKAVPGKEGHVWLAAREGGLWRSTDGGYTFEKLSNVDTAHVVGFGKAAPGQDYMAIYITGKIDNVLGFFRSDDAGKTWVRINDDEHGYGAVDTAITGDPRVYGRVYIATNGRGIVYGEPASDEPV

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 non-polymer

描述 description	CADMIUM ION
分子量 formula_weight	112.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	15

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	2081

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2cn2a1
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	d2cn2a2
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	d2cn2b1
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	d2cn2b2
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	d2cn2c1
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	d2cn2c2
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	d2cn2d1
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	d2cn2d2
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 (8 domains)

结构域编号 domain_id	2cn2A01
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	2cn2A02
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	2cn2B01
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	2cn2B02
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	2cn2C01
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	2cn2C02
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	2cn2D01
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	2cn2D02
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	100.437 Å
晶胞边长 b length_b	97.941 Å
晶胞边长 c length_c	199.122 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.62 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	19.900 Å
R 因子 r_factor	0.1780
R_work r_work	0.1760
R_free r_free	0.2100

fit	/app/data/saxs_computation/cn/2cn2/2cn2.fit
pddf	/app/data/pr_computation/cn/2cn2/2cn2.pr.out
profile	/app/data/saxs_computation/cn/2cn2/2cn2.dat