SAXSdb — 2ebs

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2ebs
沉积日期 deposition_date	2007-02-09
结构标题 title	;Crystal Structure Anaalysis of Oligoxyloglucan reducing-end-specific cellobiohydrolase (OXG-RCBH) D465N Mutant Complexed with a Xyloglucan Heptasaccharide ;
关键词 keywords	;BETA-PROPELLER, HYDROLASE, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; 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	47.39 Å
回转半径 Rg (电子) rg_electron	48.31 Å
零角强度 I(0) i0	430525000.00
分子量 molecular_weight	167700.0 kDa
排除体积 excluded_volume	207710 Å³
包络体积 envelope_volume	263470 Å³
水化壳体积 shell_volume	48977 Å³
包络直径 envelope_diameter	160.9 Å
壳层 Rg shell_rg	46.43 Å
包络 Rg envelope_rg	48.09 Å
形状 Rg shape_rg	48.31 Å
总 Rg total_rg	48.23 Å
总原子数 total_atoms	11853
残基数 n_residues	1541
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	152.7 Å
Rg (实空间) rg_real	48.21 Å
Rg 误差 (实空间) rg_real_error	1.65 Å
I(0) (实空间) i0_real	4.3050e+08
I(0) 误差 (实空间) i0_real_error	7.8310e+06
Rg (倒空间) rg_reciprocal	47.40 Å
I(0) (倒空间) i0_reciprocal	430100000.0000
解质量估计 total_estimate	0.4982
解质量评级 solution_quality	SUSPICIOUS a SUSPICIOUS solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	32.4 Å
偏度 Skewness skewness	0.543
峰度 Kurtosis kurtosis	-0.620
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	38340000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.609; Stabil: 1.000; Sysdev: 0.006; Positv: 1.000; Valcen: 0.612; Smooth: 0.018

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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	Oligoxyloglucan reducing end-specific cellobiohydrolase
分子量 formula_weight	84973.7 kDa
EC 编号 ec_number	3.2.1.150
突变 mutation	D465N
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	12931

KEHYEFKNVAIGGGGYITGIVAHPKTKDLLYARTDIGGAYRWDAGTSKWIPLNDFIEAQDMNIMGTESIALDPNNPDRLYLAQGRYVGDEWAAFYVSEDRGQSFTIYESPFPMGANDMGRNNGERLAVNPFNSNEVWMGTRTEGIWKSSDRAKTWTNVTSIPDAFTNGIGYTSVIFDPERNGTIYASATAPQGMYVTHDGGVSWEPVAGQPSSWLNRTTGAFPDKKPASIAPQPMKVALTPNFLYVTYADYPGPWGVTFGEVWRQNRTSGAWDDITPRVGNSSPAPYNNQTFPAGGFCGLSVDATNPNRLVVITLDRDPGPALDSIYLSTDAGATWKDVTQLSSPSNLEGNWGHPTNAARYKDGTPVPWLDFNNGPQWGGYGAPHGTPGLTKFGWWMSAVLIDPFNPEHLMYGTGATIWATDTLSRVEKDWAPSWYLQIDGIEENAILSLRSPKSGAALLSGIGNISGMKHDDLTKPQKMFGAPQFSNLDSIDAAGNFPNVVVRAGSSGHEYDSACARGAYATDGGDAWTIFPTCPPGMNASHYQGSTIAVDASGSQIVWSTKLDEQASGPWYSHDYGKTWSVPAGDLKAQTANVLSDKVQDGTFYATDGGKFFVSTDGGKSYAAKGAGLVTGTSLMPAVNPWVAGDVWVPVPEGGLFHSTDFGASFTRVGTANATLVSVGAPKSKSDGKKASAPSAVFIWGTDKPGSDIGLYRSDDNGSTWTRVNDQEHNYSGPTMIEADPKVYGRVYLGTNGRGIVYADLTNKKSNEEKSTAKCANGQKGTHCYVKK

来源 Source

来源生物 organism	Geotrichum sp. M128
NCBI 分类编号 ncbi_taxonomy_id	203496
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)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose ;
分子量 formula_weight	1062.9 kDa
来源方法 src_method	man
拷贝数 entity_count	2

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	1078

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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	d2ebsa1
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.69.13.1 — Oligoxyloglucan reducing end-specific cellobiohydrolase

结构域编号 domain_id	d2ebsa2
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.69.13.1 — Oligoxyloglucan reducing end-specific cellobiohydrolase

结构域编号 domain_id	d2ebsb1
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.69.13.1 — Oligoxyloglucan reducing end-specific cellobiohydrolase

结构域编号 domain_id	d2ebsb2
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.69.13.1 — Oligoxyloglucan reducing end-specific cellobiohydrolase

CATH v4.4 (4 domains)

结构域编号 domain_id	2ebsA01
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	2ebsA02
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	2ebsB01
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	2ebsB02
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 (2)

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晶胞边长 a length_a	60.970 Å
晶胞边长 b length_b	147.515 Å
晶胞边长 c length_c	212.230 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	8

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	20.000 Å
R 因子 r_factor	0.1616
R_work r_work	0.1585
R_free r_free	0.2193

fit	/app/data/saxs_computation/eb/2ebs/2ebs.fit
pddf	/app/data/pr_computation/eb/2ebs/2ebs.pr.out
profile	/app/data/saxs_computation/eb/2ebs/2ebs.dat

;Crystal Structure Anaalysis of Oligoxyloglucan reducing-end-specific cellobiohydrolase (OXG-RCBH) D465N Mutant Complexed with a Xyloglucan Heptasaccharide ;

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