SAXSdb — 2d24

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2d24
沉积日期 deposition_date	2005-09-02
结构标题 title	Crystal structure of ES complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86
关键词 keywords	TIM-BARREL, RETAINING ENZYME, CATALYTIC-SITE MUTANT, CHEMICAL RESCUE, MICHAELIS COMPLEX, 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	31.76 Å
回转半径 Rg (电子) rg_electron	31.19 Å
零角强度 I(0) i0	162324000.00
分子量 molecular_weight	94871.0 kDa
排除体积 excluded_volume	115700 Å³
包络体积 envelope_volume	138610 Å³
水化壳体积 shell_volume	36890 Å³
包络直径 envelope_diameter	104.1 Å
壳层 Rg shell_rg	38.16 Å
包络 Rg envelope_rg	30.95 Å
形状 Rg shape_rg	31.17 Å
总 Rg total_rg	31.76 Å
总原子数 total_atoms	6661
残基数 n_residues	854
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	104.0 Å
Rg (实空间) rg_real	31.73 Å
Rg 误差 (实空间) rg_real_error	0.87 Å
I(0) (实空间) i0_real	1.6230e+08
I(0) 误差 (实空间) i0_real_error	2.5510e+06
Rg (倒空间) rg_reciprocal	31.75 Å
I(0) (倒空间) i0_reciprocal	162300000.0000
解质量估计 total_estimate	0.8969
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	37.4 Å
偏度 Skewness skewness	0.255
峰度 Kurtosis kurtosis	-0.527
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	48260000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.924

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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 (7)

Entity 1 polymer

描述 description	ENDO-1,4-BETA-D-XYLANASE
分子量 formula_weight	46773.2 kDa
EC 编号 ec_number	3.2.1.8
突变 mutation	N127S and E128H
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	7333

AESTLGAAAAQSGRYFGTAIASGKLGDSAYTTIASREFNMVTAENEMKIDATEPQRGQFNFSAGDRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSTLRQAMIDHINGVMGHYKGKIAQWDVVSHAFSDDGSGGRRDSNLQRTGNDWIEVAFRTARAADPAAKLCYNDYNIENWTWAKTQGVYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGASSSTYAAVTNDCLAVSRCLGITVWGVRDTDSWRSGDTPLLFNGDGSKKAAYTAVLNALNGGSSTPPPSGGGQIKGVGSGRCLDVPNASTTDGTQVQLYDCHSATNQQWTYTDAGELRVYGDKCLDAAGTGNGTKVQIYSCWGGDNQKWRLNSDGSIVGVQSGLCLDAVGGGTANGTLIQLYSCSNGSNQRWTRT

来源 Source

来源生物 organism	Streptomyces olivaceoviridis
NCBI 分类编号 ncbi_taxonomy_id	1921
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose
分子量 formula_weight	678.6 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 3 branched

描述 description	alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose
分子量 formula_weight	546.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 branched

描述 description	alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose
分子量 formula_weight	282.2 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 7 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	672

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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	d2d24a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.8 — (Trans)glycosidases
家族 Family family	c.1.8.3 — beta-glycanases

结构域编号 domain_id	d2d24a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.42 — beta-Trefoil
超家族 Superfamily superfamily	b.42.2 — Ricin B-like lectins
家族 Family family	b.42.2.0 — automated matches

结构域编号 domain_id	d2d24b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.8 — (Trans)glycosidases
家族 Family family	c.1.8.3 — beta-glycanases

结构域编号 domain_id	d2d24b2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.42 — beta-Trefoil
超家族 Superfamily superfamily	b.42.2 — Ricin B-like lectins
家族 Family family	b.42.2.0 — automated matches

CATH v4.4 (4 domains)

结构域编号 domain_id	2d24A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

结构域编号 domain_id	2d24A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	2d24B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

结构域编号 domain_id	2d24B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
同源超家族 H-superfamily homologous superfamily	50 —

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7. 引用文献 (6)

Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86

J.Biochem. (2009)

PMID: 19279191 · DOI: 10.1093/jb/mvp047 PRIMARY

Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86

J.Biol.Chem. (2004)

PMID: 14670957 · DOI: 10.1074/jbc.M312293200

;Crystal structures of the sugar complexes of Streptomyces olivaceoviridis E-86 xylanase: sugar binding structure of the family 13 carbohydrate binding module ;

J.Mol.Biol. (2002)

PMID: 11829503 · DOI: 10.1006/jmbi.2001.5338

Crystal structure of Streptomyces olivaceoviridis E-86 beta-xylanase containing xylan-binding domain

J.Mol.Biol. (2000)

PMID: 10884353 · DOI: 10.1006/jmbi.2000.3877

;Significant enhancement in the binding of p-nitrophenyl-beta-D-xylobioside by the E128H mutant F/10 xylanase from Streptomyces olivaceoviridis E-86 ;

Febs Lett. (1999)

PMID: 10359093 · DOI: 10.1016/S0014-5793(99)00498-6

PCR Cloning and Expression of the F/10 Family Xylanse Gene from Streptomyces olivaceoviridis E-86

J.FERMENT.BIOENG. (1998)

DOI: 10.1016/S0922-338X(98)80147-5

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晶胞边长 a length_a	75.704 Å
晶胞边长 b length_b	94.090 Å
晶胞边长 c length_c	138.366 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	1.850 Å
最低分辨率 resolution_low	36.510 Å
R 因子 r_factor	0.1770
R_work r_work	0.1770
R_free r_free	0.1990

fit	/app/data/saxs_computation/d2/2d24/2d24.fit
pddf	/app/data/pr_computation/d2/2d24/2d24.pr.out
profile	/app/data/saxs_computation/d2/2d24/2d24.dat

Crystal structure of ES complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution