1q9x

Crystal structure of Enterobacteria phage RB69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA

Method: X-RAY DIFFRACTION D_max: 215.1 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	1q9x
沉积日期 deposition_date	2003-08-26
结构标题 title	Crystal structure of Enterobacteria phage RB69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA
关键词 keywords	PROTEIN-DNA COMPLEX, Transferase, replication-DNA COMPLEX; Transferase,replication/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	79.77 Å
回转半径 Rg (电子) rg_electron	80.17 Å
零角强度 I(0) i0	3197480000.00
分子量 molecular_weight	459300.0 kDa
排除体积 excluded_volume	566420 Å³
包络体积 envelope_volume	1030300 Å³
水化壳体积 shell_volume	117090 Å³
包络直径 envelope_diameter	271.6 Å
壳层 Rg shell_rg	65.98 Å
包络 Rg envelope_rg	76.70 Å
形状 Rg shape_rg	80.15 Å
总 Rg total_rg	79.97 Å
总原子数 total_atoms	32221
残基数 n_residues	3736
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	215.1 Å
Rg (实空间) rg_real	77.75 Å
Rg 误差 (实空间) rg_real_error	0.98 Å
I(0) (实空间) i0_real	3.1420e+09
I(0) 误差 (实空间) i0_real_error	5.8280e+07
Rg (倒空间) rg_reciprocal	78.06 Å
I(0) (倒空间) i0_reciprocal	3182000000.0000
解质量估计 total_estimate	0.8533
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	107.6 Å
偏度 Skewness skewness	0.257
峰度 Kurtosis kurtosis	-0.666
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	0.0661
最高正则化参数 α highest_alpha	126300000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 0.979; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.410

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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 (8)

Entity 1 polymer

描述 description	5'-GCGGACTGCTTAC(dideoxycytidine)-3'
分子量 formula_weight	5566.6 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,F,G,H
原子数 atom_count	32756

ACGGTAAGCAGTCCGCGG

Entity 2 polymer

描述 description	5'-AC(tetrahydrofuran)GGTAAGCAGTCCGCGG-3'
分子量 formula_weight	3967.6 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	I,J,K,L

GCGGACTGCTTAC

Entity 3 polymer

描述 description	DNA polymerase
分子量 formula_weight	104655.1 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

Entity 4 non-polymer

描述 description	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
分子量 formula_weight	198.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 non-polymer

描述 description	2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
分子量 formula_weight	291.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 non-polymer

描述 description	2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
分子量 formula_weight	347.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 7 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 8 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	535

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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	d1q9xa1
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	d1q9xa2
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	d1q9xb1
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	d1q9xb2
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	d1q9xc1
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	d1q9xc2
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	d1q9xd1
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	d1q9xd2
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	1q9xA01
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	1q9xA02
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	1q9xA03
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	1q9xA04
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	1q9xA05
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	1q9xA06
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	1q9xB01
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	1q9xB02
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	1q9xB03
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	1q9xB04
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	1q9xB05
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	1q9xB06
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	1q9xC01
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	1q9xC02
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	1q9xC03
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	1q9xC04
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	1q9xC05
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	1q9xC06
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	1q9xD01
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	1q9xD02
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	1q9xD03
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	1q9xD04
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	1q9xD05
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	1q9xD06
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	131.948 Å
晶胞边长 b length_b	122.237 Å
晶胞边长 c length_c	165.358 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.85 °
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	2.690 Å
最低分辨率 resolution_low	47.000 Å
R 因子 r_factor	0.2188
R_work r_work	0.2151
R_free r_free	0.2879

Crystal structure of Enterobacteria phage RB69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA

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 (8)

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 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 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)

fit	/app/data/saxs_computation/q9/1q9x/1q9x.fit
pddf	/app/data/pr_computation/q9/1q9x/1q9x.pr.out
profile	/app/data/saxs_computation/q9/1q9x/1q9x.dat