1xi1

Phi29 DNA polymerase ssDNA complex, monoclinic crystal form

Method: X-RAY DIFFRACTION D_max: 114.3 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	1xi1
沉积日期 deposition_date	2004-09-21
结构标题 title	Phi29 DNA polymerase ssDNA complex, monoclinic crystal form
关键词 keywords	DNA polymerase, protein-primed, strand displacement, processivity, replication, 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	35.26 Å
回转半径 Rg (电子) rg_electron	34.74 Å
零角强度 I(0) i0	252372000.00
分子量 molecular_weight	134090.0 kDa
排除体积 excluded_volume	170330 Å³
包络体积 envelope_volume	226530 Å³
水化壳体积 shell_volume	54074 Å³
包络直径 envelope_diameter	117.4 Å
壳层 Rg shell_rg	41.82 Å
包络 Rg envelope_rg	33.93 Å
形状 Rg shape_rg	34.72 Å
总 Rg total_rg	35.32 Å
总原子数 total_atoms	9458
残基数 n_residues	1147
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	114.3 Å
Rg (实空间) rg_real	35.16 Å
Rg 误差 (实空间) rg_real_error	0.69 Å
I(0) (实空间) i0_real	2.5240e+08
I(0) 误差 (实空间) i0_real_error	4.1460e+06
Rg (倒空间) rg_reciprocal	35.23 Å
I(0) (倒空间) i0_reciprocal	252400000.0000
解质量估计 total_estimate	0.8894
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	43.2 Å
偏度 Skewness skewness	0.266
峰度 Kurtosis kurtosis	-0.371
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	40030000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.921

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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(PTPTPTPTP*T)-3'
分子量 formula_weight	1476.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	C,D
原子数 atom_count	9693

TTTTT

Entity 2 polymer

描述 description	DNA polymerase
分子量 formula_weight	66720.9 kDa
EC 编号 ec_number	2.7.7.7
突变 mutation	D12A D66A
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

MKHMPRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK

来源 Source

来源生物 organism	Bacillus phage phi29
NCBI 分类编号 ncbi_taxonomy_id	10756
宿主生物 host_organism	Escherichia coli

Entity 3 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	2

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	235

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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	d1xi1a1
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	d1xi1a2
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	d1xi1b1
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	d1xi1b2
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	1xi1A01
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	1xi1A02
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	1xi1A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1770 — TPR 1 domain of DNA polymerase
同源超家族 H-superfamily homologous superfamily	10 — TPR 1 domain of DNA polymerase

结构域编号 domain_id	1xi1A04
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	1xi1A05
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	80 — Rhinovirus 14, subunit 4
同源超家族 H-superfamily homologous superfamily	20 — DNA polymerase; domain 5

结构域编号 domain_id	1xi1A06
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	80 — Rhinovirus 14, subunit 4
同源超家族 H-superfamily homologous superfamily	30 — DNA polymerase; domain 6

结构域编号 domain_id	1xi1B01
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	1xi1B02
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	1xi1B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1770 — TPR 1 domain of DNA polymerase
同源超家族 H-superfamily homologous superfamily	10 — TPR 1 domain of DNA polymerase

结构域编号 domain_id	1xi1B04
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	1xi1B05
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	80 — Rhinovirus 14, subunit 4
同源超家族 H-superfamily homologous superfamily	20 — DNA polymerase; domain 5

结构域编号 domain_id	1xi1B06
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	80 — Rhinovirus 14, subunit 4
同源超家族 H-superfamily homologous superfamily	30 — DNA polymerase; domain 6

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7. 引用文献 (2)

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晶胞边长 a length_a	60.557 Å
晶胞边长 b length_b	170.563 Å
晶胞边长 c length_c	68.813 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	106.99 °
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	2.200 Å
最低分辨率 resolution_low	19.710 Å
R 因子 r_factor	0.2430
R_work r_work	0.2430
R_free r_free	0.2770

fit	/app/data/saxs_computation/xi/1xi1/1xi1.fit
pddf	/app/data/pr_computation/xi/1xi1/1xi1.pr.out
profile	/app/data/saxs_computation/xi/1xi1/1xi1.dat

Phi29 DNA polymerase ssDNA complex, monoclinic crystal form

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

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

CATH v4.4 (12 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)