2dy4

Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol

Method: X-RAY DIFFRACTION D_max: 196.5 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	2dy4
沉积日期 deposition_date	2006-09-06
结构标题 title	Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol
关键词 keywords	DNA polymerase, DNA lesion, thymine glycol, oxidative thymine lesion, TRANSFERASE-DNA COMPLEX; TRANSFERASE/DNA
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	60.91 Å
回转半径 Rg (电子) rg_electron	60.61 Å
零角强度 I(0) i0	3209230000.00
分子量 molecular_weight	450950.0 kDa
排除体积 excluded_volume	550930 Å³
包络体积 envelope_volume	878110 Å³
水化壳体积 shell_volume	119850 Å³
包络直径 envelope_diameter	201.0 Å
壳层 Rg shell_rg	64.09 Å
包络 Rg envelope_rg	58.10 Å
形状 Rg shape_rg	60.65 Å
总 Rg total_rg	60.54 Å
总原子数 total_atoms	31337
残基数 n_residues	3608
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	196.5 Å
Rg (实空间) rg_real	60.55 Å
Rg 误差 (实空间) rg_real_error	1.65 Å
I(0) (实空间) i0_real	3.2090e+09
I(0) 误差 (实空间) i0_real_error	6.5050e+07
Rg (倒空间) rg_reciprocal	61.18 Å
I(0) (倒空间) i0_reciprocal	3212000000.0000
解质量估计 total_estimate	0.8911
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	90.7 Å
偏度 Skewness skewness	0.016
峰度 Kurtosis kurtosis	-0.673
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	261200000.0000
实空间数据点数 n_real_points	27
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.916

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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 (4)

Entity 1 polymer

描述 description	5'-D(CPGP(CTG)PGPGPAPAPTPGPACPAPGPCPCPGPCPG)-3'
分子量 formula_weight	5600.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	E,G,I,K
原子数 atom_count	31943

CGTGGAATGACAGCCGCG

Entity 2 polymer

描述 description	5'-D(GPCPGPGPCPTPGPTCPAPTPTPCPCP*A)-3'
分子量 formula_weight	4561.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	F,H,J,L

GCGGCTGTCATTCCA

Entity 3 polymer

描述 description	DNA polymerase
分子量 formula_weight	105827.6 kDa
EC 编号 ec_number	2.7.7.7
突变 mutation	D222A, D327A
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFDF

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 BL21(DE3)

Entity 4 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	606

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6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2dy4a1
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	d2dy4a2
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	d2dy4b1
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	d2dy4b2
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	d2dy4c1
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	d2dy4c2
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	d2dy4d1
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	d2dy4d2
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 (24 domains)

结构域编号 domain_id	2dy4A01
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	2dy4A02
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	2dy4A03
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	2dy4A04
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	2dy4A05
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	2dy4A06
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	2dy4B01
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	2dy4B02
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	2dy4B03
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	2dy4B04
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	2dy4B05
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	2dy4B06
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	2dy4C01
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	2dy4C02
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	2dy4C03
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	2dy4C04
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	2dy4C05
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	2dy4C06
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	2dy4D01
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	2dy4D02
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	2dy4D03
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	2dy4D04
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	2dy4D05
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	2dy4D06
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 (1)

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晶胞边长 a length_a	132.612 Å
晶胞边长 b length_b	122.632 Å
晶胞边长 c length_c	168.695 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.31 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.650 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	—
R_work r_work	0.2290
R_free r_free	0.2810

fit	/app/data/saxs_computation/dy/2dy4/2dy4.fit
pddf	/app/data/pr_computation/dy/2dy4/2dy4.pr.out
profile	/app/data/saxs_computation/dy/2dy4/2dy4.dat

Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol

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

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 water

6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (8 domains)

CATH v4.4 (24 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)