1xje

Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dTTP-GDP complex

Method: X-RAY DIFFRACTION D_max: 122.2 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	1xje
沉积日期 deposition_date	2004-09-23
结构标题 title	Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dTTP-GDP complex
关键词 keywords	;ribonucleotide reductase, 10 alpha-beta barrel, protein-nucleotide complex, substrate specificity, allosteric regulation, 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	37.32 Å
回转半径 Rg (电子) rg_electron	37.20 Å
零角强度 I(0) i0	301888000.00
分子量 molecular_weight	143890.0 kDa
排除体积 excluded_volume	181180 Å³
包络体积 envelope_volume	225920 Å³
水化壳体积 shell_volume	50131 Å³
包络直径 envelope_diameter	124.0 Å
壳层 Rg shell_rg	43.87 Å
包络 Rg envelope_rg	37.06 Å
形状 Rg shape_rg	37.20 Å
总 Rg total_rg	37.59 Å
总原子数 total_atoms	10123
残基数 n_residues	1245
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	122.2 Å
Rg (实空间) rg_real	37.40 Å
Rg 误差 (实空间) rg_real_error	0.84 Å
I(0) (实空间) i0_real	3.0190e+08
I(0) 误差 (实空间) i0_real_error	4.6440e+06
Rg (倒空间) rg_reciprocal	37.36 Å
I(0) (倒空间) i0_reciprocal	301900000.0000
解质量估计 total_estimate	0.8824
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	37.8 Å
偏度 Skewness skewness	0.334
峰度 Kurtosis kurtosis	-0.621
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	68150000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.860

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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	ribonucleotide reductase, B12-dependent
分子量 formula_weight	73374.2 kDa
EC 编号 ec_number	1.17.4.1
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	10914

MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVARVVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVVKQGSRRRGALMGILNINHPDIEEFIDAKKENTGEAVLNFFNLSVGFPMDKKEILKLYEEDGELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYPHRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAVRFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEARDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGMSNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAYTRFVTKEDGTKEPLLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKVFVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEALRTNVRGITVYRDGSLQTQVLTKALKT

来源 Source

来源生物 organism	Thermotoga maritima
NCBI 分类编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	GUANOSINE-5'-DIPHOSPHATE
分子量 formula_weight	443.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	THYMIDINE-5'-TRIPHOSPHATE
分子量 formula_weight	482.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	1

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	791

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6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id	1xjeA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1xjeB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
同源超家族 H-superfamily homologous superfamily	20 —

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7. 引用文献 (1)

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晶胞边长 a length_a	119.391 Å
晶胞边长 b length_b	124.376 Å
晶胞边长 c length_c	107.243 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.68 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	18.000 Å
R 因子 r_factor	0.1845
R_work r_work	0.1824
R_free r_free	0.2227

fit	/app/data/saxs_computation/xj/1xje/1xje.fit
pddf	/app/data/pr_computation/xj/1xje/1xje.pr.out
profile	/app/data/saxs_computation/xj/1xje/1xje.dat