1waf

DNA POLYMERASE FROM BACTERIOPHAGE RB69

Method: X-RAY DIFFRACTION D_max: 154.1 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	1waf
沉积日期 deposition_date	1997-04-13
结构标题 title	DNA POLYMERASE FROM BACTERIOPHAGE RB69
关键词 keywords	NUCLEOTIDYLTRANSFERASE, RB69 DNA POLYMERASE (GP43); NUCLEOTIDYLTRANSFERASE
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	45.99 Å
回转半径 Rg (电子) rg_electron	45.58 Å
零角强度 I(0) i0	620124000.00
分子量 molecular_weight	209730.0 kDa
排除体积 excluded_volume	264030 Å³
包络体积 envelope_volume	377290 Å³
水化壳体积 shell_volume	69698 Å³
包络直径 envelope_diameter	160.6 Å
壳层 Rg shell_rg	49.81 Å
包络 Rg envelope_rg	44.30 Å
形状 Rg shape_rg	45.56 Å
总 Rg total_rg	45.84 Å
总原子数 total_atoms	14800
残基数 n_residues	1806
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	154.1 Å
Rg (实空间) rg_real	45.99 Å
Rg 误差 (实空间) rg_real_error	1.23 Å
I(0) (实空间) i0_real	6.2010e+08
I(0) 误差 (实空间) i0_real_error	1.1270e+07
Rg (倒空间) rg_reciprocal	45.99 Å
I(0) (倒空间) i0_reciprocal	620100000.0000
解质量估计 total_estimate	0.8881
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	54.4 Å
偏度 Skewness skewness	0.312
峰度 Kurtosis kurtosis	-0.431
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	38600000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.891

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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 (2)

Entity 1 polymer

描述 description	DNA POLYMERASE
分子量 formula_weight	104743.2 kDa
EC 编号 ec_number	2.7.7.7
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	14800

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFDIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIDVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFDF

来源 Source

来源生物 organism	Enterobacteria phage RB69
NCBI 分类编号 ncbi_taxonomy_id	12353
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	GUANOSINE
分子量 formula_weight	283.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1wafa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.3 — Ribonuclease H-like
家族 Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

结构域编号 domain_id	d1wafa2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.8 — DNA/RNA polymerases
超家族 Superfamily superfamily	e.8.1 — DNA/RNA polymerases
家族 Family family	e.8.1.1 — DNA polymerase I

结构域编号 domain_id	d1wafb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.3 — Ribonuclease H-like
家族 Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

结构域编号 domain_id	d1wafb2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.8 — DNA/RNA polymerases
超家族 Superfamily superfamily	e.8.1 — DNA/RNA polymerases
家族 Family family	e.8.1.1 — DNA polymerase I

CATH v4.4 (12 domains)

结构域编号 domain_id	1wafA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	342 — DNA Polymerase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — DNA Polymerase, chain B, domain 1

结构域编号 domain_id	1wafA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

结构域编号 domain_id	1wafA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1600 — Palm domain of DNA polymerase
同源超家族 H-superfamily homologous superfamily	10 — B family DNA polymerase, palm domain

结构域编号 domain_id	1wafA04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	690 — B family DNA polymerase, finger domain

结构域编号 domain_id	1wafA05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1280 — Monooxygenase
同源超家族 H-superfamily homologous superfamily	300 —

结构域编号 domain_id	1wafA06
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1820 — Ribonuclease H-like motif
同源超家族 H-superfamily homologous superfamily	10 — DnaQ-like 3'-5' exonuclease

结构域编号 domain_id	1wafB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	342 — DNA Polymerase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — DNA Polymerase, chain B, domain 1

结构域编号 domain_id	1wafB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

结构域编号 domain_id	1wafB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1600 — Palm domain of DNA polymerase
同源超家族 H-superfamily homologous superfamily	10 — B family DNA polymerase, palm domain

结构域编号 domain_id	1wafB04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	690 — B family DNA polymerase, finger domain

结构域编号 domain_id	1wafB05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1280 — Monooxygenase
同源超家族 H-superfamily homologous superfamily	300 —

结构域编号 domain_id	1wafB06
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1820 — Ribonuclease H-like motif
同源超家族 H-superfamily homologous superfamily	10 — DnaQ-like 3'-5' exonuclease

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7. 引用文献 (5)

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晶胞边长 a length_a	88.320 Å
晶胞边长 b length_b	196.860 Å
晶胞边长 c length_c	118.310 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	92.57 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	3.200 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2740

fit	/app/data/saxs_computation/wa/1waf/1waf.fit
pddf	/app/data/pr_computation/wa/1waf/1waf.pr.out
profile	/app/data/saxs_computation/wa/1waf/1waf.dat

DNA POLYMERASE FROM BACTERIOPHAGE RB69

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