2b8q

X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with TDP

Method: X-RAY DIFFRACTION D_max: 144.6 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	2b8q
沉积日期 deposition_date	2005-10-10
结构标题 title	X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with TDP
关键词 keywords	NDK, TDP, phosphotranferase, TRANSFERASE; TRANSFERASE
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	50.72 Å
回转半径 Rg (电子) rg_electron	51.32 Å
零角强度 I(0) i0	129935000.00
分子量 molecular_weight	92632.0 kDa
排除体积 excluded_volume	115050 Å³
包络体积 envelope_volume	173440 Å³
水化壳体积 shell_volume	28683 Å³
包络直径 envelope_diameter	155.0 Å
壳层 Rg shell_rg	53.96 Å
包络 Rg envelope_rg	48.93 Å
形状 Rg shape_rg	51.34 Å
总 Rg total_rg	51.34 Å
总原子数 total_atoms	6499
残基数 n_residues	788
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	144.6 Å
Rg (实空间) rg_real	51.12 Å
Rg 误差 (实空间) rg_real_error	1.68 Å
I(0) (实空间) i0_real	1.2990e+08
I(0) 误差 (实空间) i0_real_error	2.5430e+06
Rg (倒空间) rg_reciprocal	50.35 Å
I(0) (倒空间) i0_reciprocal	129800000.0000
解质量估计 total_estimate	0.6357
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	28.0 Å
偏度 Skewness skewness	0.244
峰度 Kurtosis kurtosis	-1.235
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2801000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.366; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.163; 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 (5)

Entity 1 polymer

描述 description	Probable nucleoside diphosphate kinase
分子量 formula_weight	16301.5 kDa
EC 编号 ec_number	2.7.4.6
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	6652

YKKAGLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPETKMETDN

来源 Source

来源生物 organism	Mimivirus
NCBI 分类编号 ncbi_taxonomy_id	315393
宿主生物 host_organism	Escherichia coli

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	6

Entity 3 non-polymer

描述 description	THYMIDINE-5'-DIPHOSPHATE
分子量 formula_weight	402.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 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	153

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d2b8qa1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.6 — Nucleoside diphosphate kinase, NDK
家族 Family family	d.58.6.1 — Nucleoside diphosphate kinase, NDK

结构域编号 domain_id	d2b8qa2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2b8qb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.6 — Nucleoside diphosphate kinase, NDK
家族 Family family	d.58.6.1 — Nucleoside diphosphate kinase, NDK

结构域编号 domain_id	d2b8qb2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2b8qc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.6 — Nucleoside diphosphate kinase, NDK
家族 Family family	d.58.6.1 — Nucleoside diphosphate kinase, NDK

结构域编号 domain_id	d2b8qc2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2b8qd1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.6 — Nucleoside diphosphate kinase, NDK
家族 Family family	d.58.6.1 — Nucleoside diphosphate kinase, NDK

结构域编号 domain_id	d2b8qd2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2b8qe1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.6 — Nucleoside diphosphate kinase, NDK
家族 Family family	d.58.6.1 — Nucleoside diphosphate kinase, NDK

结构域编号 domain_id	d2b8qe2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2b8qf1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.6 — Nucleoside diphosphate kinase, NDK
家族 Family family	d.58.6.1 — Nucleoside diphosphate kinase, NDK

结构域编号 domain_id	d2b8qf2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

结构域编号 domain_id	2b8qA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	141 — Nucleoside diphosphate kinase-like domain

结构域编号 domain_id	2b8qB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	141 — Nucleoside diphosphate kinase-like domain

结构域编号 domain_id	2b8qC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	141 — Nucleoside diphosphate kinase-like domain

结构域编号 domain_id	2b8qD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	141 — Nucleoside diphosphate kinase-like domain

结构域编号 domain_id	2b8qE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	141 — Nucleoside diphosphate kinase-like domain

结构域编号 domain_id	2b8qF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	141 — Nucleoside diphosphate kinase-like domain

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7. 引用文献 (1)

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晶胞边长 a length_a	80.390 Å
晶胞边长 b length_b	153.352 Å
晶胞边长 c length_c	185.491 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	48

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	29.550 Å
R 因子 r_factor	0.1990
R_work r_work	0.1990
R_free r_free	0.2310

fit	/app/data/saxs_computation/b8/2b8q/2b8q.fit
pddf	/app/data/pr_computation/b8/2b8q/2b8q.pr.out
profile	/app/data/saxs_computation/b8/2b8q/2b8q.dat