1hk8

STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DGTP

Method: X-RAY DIFFRACTION D_max: 92.3 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hk8
沉积日期 deposition_date	2003-03-06
结构标题 title	STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DGTP
关键词 keywords	OXIDOREDUCTASE, REDUCTASE, ALLOSTERIC REGULATION, SUBSTRATE SPECIFICITY; 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	25.28 Å
回转半径 Rg (电子) rg_electron	24.29 Å
零角强度 I(0) i0	68686100.00
分子量 molecular_weight	63902.0 kDa
排除体积 excluded_volume	79532 Å³
包络体积 envelope_volume	95697 Å³
水化壳体积 shell_volume	32062 Å³
包络直径 envelope_diameter	96.1 Å
壳层 Rg shell_rg	32.13 Å
包络 Rg envelope_rg	24.68 Å
形状 Rg shape_rg	24.26 Å
总 Rg total_rg	25.18 Å
总原子数 total_atoms	4475
残基数 n_residues	561
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	92.3 Å
Rg (实空间) rg_real	25.19 Å
Rg 误差 (实空间) rg_real_error	0.86 Å
I(0) (实空间) i0_real	6.8690e+07
I(0) 误差 (实空间) i0_real_error	1.0250e+06
Rg (倒空间) rg_reciprocal	25.22 Å
I(0) (倒空间) i0_reciprocal	68690000.0000
解质量估计 total_estimate	0.6573
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	90.8 Å
偏度 Skewness skewness	0.297
峰度 Kurtosis kurtosis	-0.103
角度范围 angular_range	— – 0.3150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12900000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.627; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.957; Smooth: 0.976

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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 (5)

Entity 1 polymer

描述 description	ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE
分子量 formula_weight	68055.6 kDa
EC 编号 ec_number	1.17.4.2
突变 mutation	YES
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	4703

MTIEKEIEGLIHKTNKDLLNENANKDSRVFPTQRDLMAGIVSKHIAKNMVPSFIMKAHESGIIHVHDIDYSPALPFTNCCLVDLKGMLENGFKLGNAQIETPKSIGVATAIMAQITAQVASHQYGGTTFANVDKVLSPYVKRTYAKHIEDAEKWQIADALNYAQSKTEKDVYDAFQAYEYEVNTLFSSNGQTPFVTITFGTGTDWTERMIQKAILKNRIKGLGRDGITPIFPKLVMFVEEGVNLYKDDPNYDIKQLALECASKRMYPDIISAKNNKAITGSSVPVSPMGCRSFLSVWKDSTGNEILDGRNNLGVVTLNLPRIALDSYIGTQFNEQKFVELFNERMDLCFEALMCRISSLKGVKATVAPILYQEGAFGVRLKPDDDIIELFKNGRSSVSLGYIGIHELNILVGRDIGREILTKMNAHLKQWTERTGFAFSLYSTPAENLCYRFCKLDTEKYGSVKDVTDKGWYTNSFHVSVEENITPFEKISREAPYHFIATGGHISYVELPDMKNNLKGLEAVWDYAAQHLDYFGVNMPVDKCFTCGSTHEMTPTENGFVCSICGETDPKKMNTIRRTCAYLGNPNERGFNLGKNKEIMHRVKHQ

来源 Source

来源生物 organism	BACTERIOPHAGE T4
NCBI 分类编号 ncbi_taxonomy_id	10665
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	228

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1hk8a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.7 — PFL-like glycyl radical enzymes
超家族 Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
家族 Family family	c.7.1.3 — Class III anaerobic ribonucleotide reductase NRDD subunit

CATH v4.4 (1 domains)

结构域编号 domain_id	1hk8A00
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 (2)

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晶胞边长 a length_a	98.163 Å
晶胞边长 b length_b	98.163 Å
晶胞边长 c length_c	246.131 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 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	2.450 Å
最低分辨率 resolution_low	20.080 Å
R 因子 r_factor	—
R_work r_work	0.2040
R_free r_free	0.2460

fit	/app/data/saxs_computation/hk/1hk8/1hk8.fit
pddf	/app/data/pr_computation/hk/1hk8/1hk8.pr.out
profile	/app/data/saxs_computation/hk/1hk8/1hk8.dat