8q9x

The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum with molecular oxygen at 1.05 A resolution

Method: X-RAY DIFFRACTION D_max: 103.4 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8q9x
沉积日期 deposition_date	2023-08-22
结构标题 title	The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum with molecular oxygen at 1.05 A resolution
关键词 keywords	;Thiocyanate dehydrogenase, copper enzyme, trinuclear copper center, atomic resolution, conformational changes, complex with molecular oxygen, Pelomicrobium methylotrophicum, OXIDOREDUCTASE ;; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	30.51 Å
回转半径 Rg (电子) rg_electron	29.94 Å
零角强度 I(0) i0	162945000.00
分子量 molecular_weight	103820.0 kDa
排除体积 excluded_volume	130440 Å³
包络体积 envelope_volume	147020 Å³
水化壳体积 shell_volume	40675 Å³
包络直径 envelope_diameter	105.2 Å
壳层 Rg shell_rg	37.47 Å
包络 Rg envelope_rg	30.21 Å
形状 Rg shape_rg	29.92 Å
总 Rg total_rg	30.62 Å
总原子数 total_atoms	14135
残基数 n_residues	937
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

▼

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

最大尺寸 Dmax dmax	103.4 Å
Rg (实空间) rg_real	30.60 Å
Rg 误差 (实空间) rg_real_error	0.87 Å
I(0) (实空间) i0_real	1.6290e+08
I(0) 误差 (实空间) i0_real_error	2.5940e+06
Rg (倒空间) rg_reciprocal	30.57 Å
I(0) (倒空间) i0_reciprocal	162900000.0000
解质量估计 total_estimate	0.6767
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	29.8 Å
偏度 Skewness skewness	0.449
峰度 Kurtosis kurtosis	-0.374
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	176500000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.763; Stabil: 0.999; Sysdev: 0.193; Positv: 1.000; Valcen: 0.942; Smooth: 0.987

▶

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

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	Twin-arginine translocation signal domain-containing protein
分子量 formula_weight	54093.3 kDa
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	16019

MGSDKIHHHHHHENLYFQGHMARTTKIEEFYAQFGKYILLVPGKFTGTVAAHDLSTGRTLAWLAGWNYGDTNPIMHHMAAFPSPDPYKGFEFIVNTQGGKNLFIYGIPTTVKEPGEGFNIYRVRYDGTKFNLVSNIAEKTGLGLGVHVTATPDGKGFAVADGQKDIFAEFDLATESVRTAFLVDWKPNNSDLKRAWLEGGTMTITRLKPTLPGGKYDYTGTKGCKIDWELVPGGELFLEEGKVTGTRQTNVVALDAFVYDPRGRWGALSARLPGVAIIFDRQDWEPVVALVGAKGEPSSLPVKKVASDTWEIKMDKVVTPAHQAGFSPDGKNFLFMNGVRQNNIMVWDTSNHADPTKWTKKAVVEDPGWRGSYPNTFHMVFTPDGRKVYVTLWWPSPTPNGIAVVDARNWKLLKSVDIGPDMHTLAITYDGKYVVGVFSGYQKTASGIVIMDTKSDEVVGILPSVGGHHDCVIVPKTVEDLRCSRCTTT

来源 Source

来源生物 organism	Pelomicrobium methylotrophicum
NCBI 分类编号 ncbi_taxonomy_id	2602750
宿主生物 host_organism	Escherichia coli

Entity 2 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	3

Entity 3 non-polymer

描述 description	OXYGEN MOLECULE
分子量 formula_weight	32.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	8

Entity 5 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	1319

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	66.840 Å
晶胞边长 b length_b	96.570 Å
晶胞边长 c length_c	147.450 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	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.050 Å
最低分辨率 resolution_low	45.930 Å
R 因子 r_factor	0.1093
R_work r_work	0.1085
R_free r_free	0.1258

fit	/app/data/saxs_computation/q9/8q9x/8q9x.fit
pddf	/app/data/pr_computation/q9/8q9x/8q9x.pr.out
profile	/app/data/saxs_computation/q9/8q9x/8q9x.dat

The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum with molecular oxygen at 1.05 A resolution

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