8p3m

The structure of thiocyanate dehydrogenase mutant form with Lys 281 replaced by Ala from Thioalkalivibrio paradoxus

Method: X-RAY DIFFRACTION D_max: 230.3 Å Quality: EXCELLENT

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	8p3m
沉积日期 deposition_date	2023-05-18
结构标题 title	The structure of thiocyanate dehydrogenase mutant form with Lys 281 replaced by Ala from Thioalkalivibrio paradoxus
关键词 keywords	Thiocyanate dehydrogenase, Thioalkalivibrio paradoxus, Recombinant protein, Surface amino acid residue mutation, 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	85.98 Å
回转半径 Rg (电子) rg_electron	86.57 Å
零角强度 I(0) i0	9387200000.00
分子量 molecular_weight	824160.0 kDa
排除体积 excluded_volume	1028000 Å³
包络体积 envelope_volume	1505000 Å³
水化壳体积 shell_volume	148990 Å³
包络直径 envelope_diameter	285.6 Å
壳层 Rg shell_rg	79.99 Å
包络 Rg envelope_rg	83.04 Å
形状 Rg shape_rg	86.57 Å
总 Rg total_rg	86.49 Å
总原子数 total_atoms	58012
残基数 n_residues	7472
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	230.3 Å
Rg (实空间) rg_real	82.52 Å
Rg 误差 (实空间) rg_real_error	0.79 Å
I(0) (实空间) i0_real	8.9880e+09
I(0) 误差 (实空间) i0_real_error	1.8140e+08
Rg (倒空间) rg_reciprocal	83.12 Å
I(0) (倒空间) i0_reciprocal	9307000000.0000
解质量估计 total_estimate	0.9072
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	76.8 Å
偏度 Skewness skewness	0.323
峰度 Kurtosis kurtosis	-0.786
角度范围 angular_range	— – 0.0900 Å⁻¹
当前正则化参数 α current_alpha	1.1940
最高正则化参数 α highest_alpha	252700000.0000
实空间数据点数 n_real_points	19
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.992; Stabil: 0.972; Sysdev: 1.000; Positv: 1.000; Valcen: 0.903; 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 (6)

Entity 1 polymer

描述 description	Twin-arginine translocation signal domain-containing protein
分子量 formula_weight	54944.6 kDa
突变 mutation	K281A
来源方法 src_method	man
拷贝数 entity_count	16

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D,G,J,M,P,S,V,Y,2,5,8,x,e,h,k
原子数 atom_count	60462

MSYYHHHHHHDYDIPTTENLYFQGAMGKYVKVQDFYDQLGKYVLVAPGKFSGTVAATDLSTGWTMAWLAAWNYGDTCPIMHHMAAFPSPDPYKEFEFVVNTQGGKNLFIYGVPVTVEDPGEGMKIYRIKYDGTRMNLQRDAAEVSGLGLGVHVTITPEADGYAVGDGQKDICAEFDRETDMVRYAWAFDWDPNVKDLKRAWLDGGTMTIKRLKPTLPGGRYDLQGSAGNKIDWELVPGGELAIEDGKVSGDRPLHSVANDALVFDPRGKWAVASMRLPGVCVVFDRENQVPVAVLAGPKGTPSQFQLVKVDDDTWTVDIPEVISAGHQAGFSPDGQSFLFMNSLRQNNIMVWDSSNHDDPTTWEKKAVVESPDWRGAYPNTFHMVFTPDAKKIYVTMWWPSPTPNGIAVIDAVNWEVLKEVDLGPDMHTLAITYDGKFVVGTLSGYQNTASAIVVMETETDEVLGFLPSPMGHHDNVIVPRTLEDLRISRSTTT

来源 Source

来源生物 organism	Thioalkalivibrio paradoxus ARh 1
NCBI 分类编号 ncbi_taxonomy_id	713585
宿主生物 host_organism	Escherichia coli

Entity 2 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	17

Entity 3 non-polymer

描述 description	BORIC ACID
分子量 formula_weight	61.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	32

Entity 5 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	2

Entity 6 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	2420

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7. 引用文献 (1)

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晶胞边长 a length_a	98.150 Å
晶胞边长 b length_b	142.420 Å
晶胞边长 c length_c	294.400 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.07 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	32

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	2.070 Å
最低分辨率 resolution_low	49.120 Å
R 因子 r_factor	0.1816
R_work r_work	0.1788
R_free r_free	0.2336

fit	/app/data/saxs_computation/p3/8p3m/8p3m.fit
pddf	/app/data/pr_computation/p3/8p3m/8p3m.pr.out
profile	/app/data/saxs_computation/p3/8p3m/8p3m.dat