8ic1

endo-alpha-D-arabinanase EndoMA1 D51N mutant from Microbacterium arabinogalactanolyticum in complex with arabinooligosaccharides

Method: X-RAY DIFFRACTION D_max: 128.5 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	8ic1
沉积日期 deposition_date	2023-02-10
结构标题 title	endo-alpha-D-arabinanase EndoMA1 D51N mutant from Microbacterium arabinogalactanolyticum in complex with arabinooligosaccharides
关键词 keywords	Glycoside Hydrolase, 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	40.21 Å
回转半径 Rg (电子) rg_electron	39.83 Å
零角强度 I(0) i0	723694000.00
分子量 molecular_weight	216300.0 kDa
排除体积 excluded_volume	267880 Å³
包络体积 envelope_volume	326180 Å³
水化壳体积 shell_volume	66613 Å³
包络直径 envelope_diameter	139.7 Å
壳层 Rg shell_rg	47.14 Å
包络 Rg envelope_rg	39.45 Å
形状 Rg shape_rg	39.80 Å
总 Rg total_rg	40.28 Å
总原子数 total_atoms	15260
残基数 n_residues	1916
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	128.5 Å
Rg (实空间) rg_real	40.08 Å
Rg 误差 (实空间) rg_real_error	1.16 Å
I(0) (实空间) i0_real	7.2370e+08
I(0) 误差 (实空间) i0_real_error	1.3270e+07
Rg (倒空间) rg_reciprocal	40.20 Å
I(0) (倒空间) i0_reciprocal	723800000.0000
解质量估计 total_estimate	0.8989
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	52.7 Å
偏度 Skewness skewness	0.180
峰度 Kurtosis kurtosis	-0.486
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	168900000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.933

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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 (11)

Entity 1 polymer

描述 description	endo-alpha-D-arabinanase
分子量 formula_weight	53730.3 kDa
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	16610

MTTSRTPATVVEKLTGPDAPNNTWGRWDIKATDLGIMWDDGAGHVLTAFGNTFGNSWTGPGGGAPPNGNWRSNVLVRSSDGDLADGMLFDWAAQGPQGVAREIIPSKKINGVEITTIPTTGISVGKRQYLGFMSVKQWGPPGVWDTNFAGIAYSDDGGGTWKVSDTRWENADGHDPFQMQAWVQKGGTIYVFGTQNGRNGPASVAKVPASKLLDKSAFRYWNGTDWSRKESDAVPVMDAPMSEMSVQYDAYSKRFLMMTLSGEDIIMRTATAPEGPWTPAQTVASSTDYPALYGGYFHPWNKDGEIYFTMSQWNPYNVYLMRLRIDRDGNIIDPNLVTDASFERSTTLGDGTNGTWAAKPNSGIDNAPAAGFTGDHRAFVRYNSGWRDIWQDVAVERGAKYRLTGFLRTSVNSDNGFFGARTLDGVPIGEINFHSVGAWTRFTVEFDAGDRDAVQVFGGVWTNSGDIWMQLDDVSLTKVRLEHHHHHH

来源 Source

来源生物 organism	Microbacterium arabinogalactanolyticum
NCBI 分类编号 ncbi_taxonomy_id	69365
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose
分子量 formula_weight	546.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

Entity 3 branched

描述 description	alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose
分子量 formula_weight	414.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 4 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	13

Entity 5 non-polymer

描述 description	TRIETHYLENE GLYCOL
分子量 formula_weight	150.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 6 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 7 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 8 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	4

Entity 9 non-polymer

描述 description	(3~{a}~{S},5~{R},6~{R},6~{a}~{S})-5-(hydroxymethyl)-2,2-dimethyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]dioxol-6-ol
分子量 formula_weight	190.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 10 non-polymer

描述 description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
分子量 formula_weight	195.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 11 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	1314

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6. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

结构域编号 domain_id	8ic1A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	260 — Galactose-binding domain-like

结构域编号 domain_id	8ic1B01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	260 — Galactose-binding domain-like

结构域编号 domain_id	8ic1C01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	260 — Galactose-binding domain-like

结构域编号 domain_id	8ic1D01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	260 — Galactose-binding domain-like

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7. 引用文献 (1)

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晶胞边长 a length_a	114.708 Å
晶胞边长 b length_b	137.731 Å
晶胞边长 c length_c	148.589 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 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	46.650 Å
R 因子 r_factor	0.1607
R_work r_work	0.1592
R_free r_free	0.1905

fit	/app/data/saxs_computation/ic/8ic1/8ic1.fit
pddf	/app/data/pr_computation/ic/8ic1/8ic1.pr.out
profile	/app/data/saxs_computation/ic/8ic1/8ic1.dat