9hun

Crystal structure of feruloyl esterase from Fusarium oxysporum G122S variant in complex with benzoic acid

Method: X-RAY DIFFRACTION D_max: 124.7 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	9hun
沉积日期 deposition_date	2024-12-23
最后修订 last_revision	2026-04-01
结构标题 title	Crystal structure of feruloyl esterase from Fusarium oxysporum G122S variant in complex with benzoic acid
关键词 keywords	Plastic degrading enzyme, 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	33.90 Å
回转半径 Rg (电子) rg_electron	34.08 Å
零角强度 I(0) i0	238994000.00
分子量 molecular_weight	122210.0 kDa
排除体积 excluded_volume	151740 Å³
包络体积 envelope_volume	183770 Å³
水化壳体积 shell_volume	46280 Å³
包络直径 envelope_diameter	134.0 Å
壳层 Rg shell_rg	39.39 Å
包络 Rg envelope_rg	34.35 Å
形状 Rg shape_rg	34.02 Å
总 Rg total_rg	34.63 Å
总原子数 total_atoms	16827
残基数 n_residues	1016
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	124.7 Å
Rg (实空间) rg_real	34.13 Å
Rg 误差 (实空间) rg_real_error	1.59 Å
I(0) (实空间) i0_real	2.3900e+08
I(0) 误差 (实空间) i0_real_error	4.4520e+06
Rg (倒空间) rg_reciprocal	33.98 Å
I(0) (倒空间) i0_reciprocal	239000000.0000
解质量估计 total_estimate	0.7980
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	37.1 Å
偏度 Skewness skewness	0.646
峰度 Kurtosis kurtosis	0.144
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	64260000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.564; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.756; Smooth: 0.929

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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 (9)

Entity 1 polymer

描述 description	Carboxylic ester hydrolase
分子量 formula_weight	62135.3 kDa
EC 编号 ec_number	3.1.1.-
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	17919

SMDTSTDICLPQDNMRPTFLLFSGLGACAAAGKGDDFAAKCAGFKTSLKLPNTKVWFTEHVPAGKNITFPDNHPTCTPKSTITDVEICRVAMFVTTGPKSNLTLEAWLPSNWTGRFLSTGNSGMAGCIQYDDVAYGAGFGFATVGANNGHNGTSAVSMYKNSGVVEDYVYRSVHTGTVLGKELTKKFYGKKHTKSYYLGCSTGGRQGWKEAQSFPDDFDGIVAGAPAMRFNGLQSRSGSFWGITGPPGAPTHLSPEEWAMVQKNVLVQCDEPLDGVADGILEDPNLCQYRPEALVCSKGQTKNCLTGPQIETVRKVFGPLYGNNGTYIYPRIPPGADQGFGFAIGEQPFPYSTEWFQYVIWNDTKWDPNTIGPNDYQKASEVNPFNVETWEGDLSKFRKRGSKIIHWHGLEDGLISSDNSMEYYNHVSATMGLSNTELDEFYRYFRVSGCGHCSGGIGANRIGNNRANLGGKEAKNNVLLALVKWVEEGQAPETITGVRYVNGATTGKVEVERRHCRYPYRNVWDRKGNYKNPDSWKCELPLEQKLISEEDLNSAVDHHHHHH

来源 Source

来源生物 organism	Fusarium oxysporum
NCBI 分类编号 ncbi_taxonomy_id	5507
宿主生物 host_organism	Komagataella pastoris

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[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	1397.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]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	1721.5 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 4 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	man
拷贝数 entity_count	6

Entity 5 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	9

Entity 6 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	16

Entity 7 non-polymer

描述 description	BENZOIC ACID
分子量 formula_weight	122.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	2

Entity 9 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	814

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7. 引用文献 (1)

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晶胞边长 a length_a	68.004 Å
晶胞边长 b length_b	89.934 Å
晶胞边长 c length_c	115.148 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.77 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	1.710 Å
最低分辨率 resolution_low	70.184 Å
R 因子 r_factor	—
R_work r_work	0.1609
R_free r_free	0.1930

fit	/app/data/saxs_computation/hu/9hun/9hun.fit
pddf	/app/data/pr_computation/hu/9hun/9hun.pr.out
profile	/app/data/saxs_computation/hu/9hun/9hun.dat