9cpm

Thermus thermophilus HB27 laccase (Tth-Lac) mutant with partial deletion of beta-hairpin sequence

Method: X-RAY DIFFRACTION D_max: 69.2 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	9cpm
沉积日期 deposition_date	2024-07-18
最后修订 last_revision	2025-02-05
结构标题 title	Thermus thermophilus HB27 laccase (Tth-Lac) mutant with partial deletion of beta-hairpin sequence
关键词 keywords	;Extremozyme, High-thermal stability, Beta-hairpin motif, Multicopper oxidase, Trinuclear center (TNC), Copper coordination, METAL BINDING PROTEIN ;; METAL BINDING PROTEIN
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	21.76 Å
回转半径 Rg (电子) rg_electron	20.57 Å
零角强度 I(0) i0	37298300.00
分子量 molecular_weight	48283.0 kDa
排除体积 excluded_volume	60934 Å³
包络体积 envelope_volume	68849 Å³
水化壳体积 shell_volume	26670 Å³
包络直径 envelope_diameter	71.7 Å
壳层 Rg shell_rg	28.39 Å
包络 Rg envelope_rg	20.89 Å
形状 Rg shape_rg	20.53 Å
总 Rg total_rg	21.64 Å
总原子数 total_atoms	3393
残基数 n_residues	428
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	69.2 Å
Rg (实空间) rg_real	21.58 Å
Rg 误差 (实空间) rg_real_error	0.28 Å
I(0) (实空间) i0_real	3.7300e+07
I(0) 误差 (实空间) i0_real_error	4.4380e+05
Rg (倒空间) rg_reciprocal	21.62 Å
I(0) (倒空间) i0_reciprocal	37300000.0000
解质量估计 total_estimate	0.8901
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	26.8 Å
偏度 Skewness skewness	0.119
峰度 Kurtosis kurtosis	-0.463
角度范围 angular_range	— – 0.3650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13500000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.861; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.992

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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 (4)

Entity 1 polymer

描述 description	Laccase
分子量 formula_weight	48073.6 kDa
EC 编号 ec_number	1.10.3.2
突变 mutation	del M295-H303, A304G
来源方法 src_method	man
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	3879

MQGPSFPEPKVVRSQGGLLSLKLSATPTPLALAGQRATLLTYGGSFPGPTLRVRPRDTVRLTLENRLPEPTNLHWHGLPISPKVDDPFLEIPPGESWTYEFTVPKELAGTFWYHPHLHGRVAPQLFAGLLGALVVESSLDAIPELREAEEHLLVLKDLALQGGRPAPHTPMDWMNGKEGDLVLVNGALRPTLVAQKATLRLRLLNASNARYYRLALQDHPLYLIAADGGFLEEPLEVSELLLAPGERAEVLVRLRKEGRFLLQALPYDRGAMGGMPQGPSRPETLLYLIAPKNPKPLPLPKALSPFPTLPAPVVTRRLVLTEDMMAARFFINGQVFDHRRVDLKGQAQTVEVWEVENQGDMDHPFHLHVHPFQVLSVGGRPFPYRAWKDVVNLKAGEVARLLVPLREKGRTVFHCHIVEHEDRGMMGVLEVG

来源 Source

来源生物 organism	Thermus thermophilus HB27
NCBI 分类编号 ncbi_taxonomy_id	262724
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	5

Entity 3 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	4

Entity 4 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	477

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7. 引用文献 (1)

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晶胞边长 a length_a	51.927 Å
晶胞边长 b length_b	66.032 Å
晶胞边长 c length_c	74.057 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	100.14 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

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	1.600 Å
最低分辨率 resolution_low	51.170 Å
R 因子 r_factor	0.1548
R_work r_work	0.1535
R_free r_free	0.1815

fit	/app/data/saxs_computation/cp/9cpm/9cpm.fit
pddf	/app/data/pr_computation/cp/9cpm/9cpm.pr.out
profile	/app/data/saxs_computation/cp/9cpm/9cpm.dat

Thermus thermophilus HB27 laccase (Tth-Lac) mutant with partial deletion of beta-hairpin sequence

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction