8gyy

Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose, 120 seconds

Method: X-RAY DIFFRACTION D_max: 173.3 Å Quality: REASONABLE

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	8gyy
沉积日期 deposition_date	2022-09-24
结构标题 title	Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose, 120 seconds
关键词 keywords	glycoside hydrolases, xylosidases, bifunctional, 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	58.80 Å
回转半径 Rg (电子) rg_electron	59.05 Å
零角强度 I(0) i0	1662680000.00
分子量 molecular_weight	341770.0 kDa
排除体积 excluded_volume	426690 Å³
包络体积 envelope_volume	576310 Å³
水化壳体积 shell_volume	83709 Å³
包络直径 envelope_diameter	189.9 Å
壳层 Rg shell_rg	56.88 Å
包络 Rg envelope_rg	58.13 Å
形状 Rg shape_rg	59.04 Å
总 Rg total_rg	59.01 Å
总原子数 total_atoms	24102
残基数 n_residues	3025
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	173.3 Å
Rg (实空间) rg_real	58.97 Å
Rg 误差 (实空间) rg_real_error	1.38 Å
I(0) (实空间) i0_real	1.6630e+09
I(0) 误差 (实空间) i0_real_error	3.1200e+07
Rg (倒空间) rg_reciprocal	58.61 Å
I(0) (倒空间) i0_reciprocal	1662000000.0000
解质量估计 total_estimate	0.6069
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	77.0 Å
偏度 Skewness skewness	0.260
峰度 Kurtosis kurtosis	-0.718
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	106200000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 0.009; Positv: 1.000; Valcen: 0.939; 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 (13)

Entity 1 polymer

描述 description	Beta-D-xylosidase/beta-D-glucosidase
分子量 formula_weight	86036.8 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	B,A,C,D
原子数 atom_count	25439

MFPARLSLAVLFSVSPALAYFSGLGLGSERSIFRRDLNSTGDESNSTQWPAPLANGGKSWASAFKKAKATVTEMTVEELANITSGVIGLCSGVTGAVTRLGIPEFCLQDGPIGPRGVHGSSQFPAGLTVAATWDRTLMYARARGMGQEFHDQGVHLALAPVTGGPLGRTPLNGRGWEGTFADPYACGEASYLSVKGLTDAGVATVSKHWIAYEQETSRNLYIDIDGVSQADIQLPISSNVDDLTMHELYMWSFAEAVRAGTNHIMCSYNRINNTHSCSNAKGLNQLLKTELNFQGGVVSDWGGQWDSVPAAENGLDVAMPGKGFLGALGDFWGATLVELINNGTVSEDLVRDKAVRILTGYYYLGQDTNPPPPFVYNTIGAPTLNATSGYRNVRKPGTAELIKEIGSASVTLLKNTGSLPLKHPQRIAVLGNDATYNVLGPNACGLANSACDIDNLNGTLTTGGGSGSALSPYTITPLEALQKRAIEDNAEIAAVVANSNTTTGAEDAIAALLPDADVTFVFLNRYSEEGADAPDFSLGGDGDNLMDLAVTYSSNVVVVIHTTGVVDIEKWADNPNVTAILVAYLPGQEAGNSLVPVLYGDVAPSGKLPWTWGKSIDDYVPNGVVYTDAYSPQSNFTEGVFIDYRWFDKMGITPRYEFGFGLSYTTFTYSNLIVDHGRWAKDYSSVMETAEPFAEWDGTNSLYDVIFTVFATITNTGNLTGSEVAQLYISIPGDNQPVRQLRGFDKIKDLPVGDSAVVTFPIRRKDVSSWSVVDQLWYVPNGDFLISVGGSSRDLPLNTTWTP

来源 Source

来源生物 organism	Lentinula edodes
通用名 common_name	shiitake mushroom
NCBI 分类编号 ncbi_taxonomy_id	5353
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	910.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 branched

描述 description	beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 branched

描述 description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	627.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 branched

描述 description	;alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-1-deoxy-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	894.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 branched

描述 description	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 8 non-polymer

描述 description	Deacetyltaxol
分子量 formula_weight	811.9 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 9 non-polymer

描述 description	D-xylose
分子量 formula_weight	150.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 10 non-polymer

描述 description	alpha-D-mannopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	22

Entity 11 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	21

Entity 12 non-polymer

描述 description	beta-D-mannopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 13 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	1294

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7. 引用文献 (1)

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晶胞边长 a length_a	228.429 Å
晶胞边长 b length_b	89.230 Å
晶胞边长 c length_c	218.087 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 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.070 Å
最低分辨率 resolution_low	35.970 Å
R 因子 r_factor	0.2211
R_work r_work	0.2191
R_free r_free	0.2590

fit	/app/data/saxs_computation/gy/8gyy/8gyy.fit
pddf	/app/data/pr_computation/gy/8gyy/8gyy.pr.out
profile	/app/data/saxs_computation/gy/8gyy/8gyy.dat