8r7i

X-ray structure of blue laccase BP76 from the termite Neocapritermes taracua

Method: X-RAY DIFFRACTION D_max: 85.7 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	8r7i
沉积日期 deposition_date	2023-11-24
结构标题 title	X-ray structure of blue laccase BP76 from the termite Neocapritermes taracua
关键词 keywords	insect, defence, protein stabilisation, glycosylation, allysine, OXIDOREDUCTASE; OXIDOREDUCTASE
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	25.57 Å
回转半径 Rg (电子) rg_electron	24.29 Å
零角强度 I(0) i0	93233600.00
分子量 molecular_weight	74352.0 kDa
排除体积 excluded_volume	92210 Å³
包络体积 envelope_volume	110440 Å³
水化壳体积 shell_volume	35653 Å³
包络直径 envelope_diameter	91.9 Å
壳层 Rg shell_rg	33.25 Å
包络 Rg envelope_rg	25.04 Å
形状 Rg shape_rg	24.26 Å
总 Rg total_rg	25.27 Å
总原子数 total_atoms	5202
残基数 n_residues	627
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	85.7 Å
Rg (实空间) rg_real	25.42 Å
Rg 误差 (实空间) rg_real_error	0.47 Å
I(0) (实空间) i0_real	9.3230e+07
I(0) 误差 (实空间) i0_real_error	1.3240e+06
Rg (倒空间) rg_reciprocal	25.47 Å
I(0) (倒空间) i0_reciprocal	93240000.0000
解质量估计 total_estimate	0.8666
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	31.8 Å
偏度 Skewness skewness	0.202
峰度 Kurtosis kurtosis	-0.297
角度范围 angular_range	— – 0.3100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22690000.0000
实空间数据点数 n_real_points	63
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.995

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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	Laccase BP76
分子量 formula_weight	70305.3 kDa
EC 编号 ec_number	1.10.3.2
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	6513

LNLESYLQPDRITRQEFLTPSNRNQCARECIAGEAPKICYYKWIAEDYVTLGPACGNCPANVTACDAPQCVVANGYEKSIRTINRMVPGPSIQVCLGDRIIVDLQNKMAGNELAIHWHGVFQKGTQYMDGVPMLTQCSILEGDVFRYDFFANNEGTLYWHSHDGLQXLDGIQGSIVVRKPKSTDLNGDTYDLDVPDHTLLILDWINTTAGSRFPGLLQRLPGQEPITFLLEDRGPTMLSSGQLIGPPVPYKEVWVESGKRFRLRLLGGLCTVTGVEFSIEDHDLTVIATDGGPIKPVTVTSFVIYSGERYDVVVNANQNPGTYWIHMKGLGVFPSPDEEVYQLALLRYSGTNEERNEVPSYNGGFARGGKVLNPQNATCAEGEGGVCVSQLVASIPDKHNVLDRKPDENIVLGFGFYNYLHGPNPFNRGIYDRFFVVPDRNLMNSVMNNISFIAPPSPPLSQGRDIPDDVYCPIGRSGFPQCPASDTMEGFCECVHLFRVPLGANVQIVMGDVTPASDLHHPFHLHGYDFFVIAMDQFRNGETLDSISSNLLETNLKQSSLPARKDTIAVPSNGYAAIRFKADNPGFWFLHCHFMYHLATGMAVVFQVGEEGDWPPVPPNFPKCGSYQPTVSLEG

Entity 2 branched

描述 description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1244.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-3-O-sulfo-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	1194.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 branched

描述 description	;3-O-sulfo-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1283.2 kDa
来源方法 src_method	man
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
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	2-methyl-5-oxidanyl-cyclohexa-2,5-diene-1,4-dione
分子量 formula_weight	138.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	1,4-benzoquinone
分子量 formula_weight	108.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 non-polymer

描述 description	2-methylcyclohexa-2,5-diene-1,4-dione
分子量 formula_weight	122.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 9 non-polymer

描述 description	HYDROXIDE ION
分子量 formula_weight	17.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 10 non-polymer

描述 description	COPPER (II) ION
分子量 formula_weight	63.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 11 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 12 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 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	1009

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7. 引用文献 (1)

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晶胞边长 a length_a	163.500 Å
晶胞边长 b length_b	163.500 Å
晶胞边长 c length_c	89.210 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	120.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 3 2 1
空间群编号 int_tables_number	150
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	47.200 Å
R 因子 r_factor	0.1325
R_work r_work	0.1322
R_free r_free	0.1448

fit	/app/data/saxs_computation/r7/8r7i/8r7i.fit
pddf	/app/data/pr_computation/r7/8r7i/8r7i.pr.out
profile	/app/data/saxs_computation/r7/8r7i/8r7i.dat