1unn

Complex of beta-clamp processivity factor and little finger domain of PolIV

Method: X-RAY DIFFRACTION D_max: 140.1 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	1unn
沉积日期 deposition_date	2003-09-11
结构标题 title	Complex of beta-clamp processivity factor and little finger domain of PolIV
关键词 keywords	BETA-CLAMP, POL IV, TRANSLESION, TRANSFERASE, DNA-DIRECTED DNA POLYMERASE, DNA REPLICATION; BETA-CLAMP
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	38.27 Å
回转半径 Rg (电子) rg_electron	37.71 Å
零角强度 I(0) i0	181731000.00
分子量 molecular_weight	107440.0 kDa
排除体积 excluded_volume	134140 Å³
包络体积 envelope_volume	182490 Å³
水化壳体积 shell_volume	41174 Å³
包络直径 envelope_diameter	149.2 Å
壳层 Rg shell_rg	43.05 Å
包络 Rg envelope_rg	36.80 Å
形状 Rg shape_rg	37.75 Å
总 Rg total_rg	37.96 Å
总原子数 total_atoms	7538
残基数 n_residues	955
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	140.1 Å
Rg (实空间) rg_real	38.44 Å
Rg 误差 (实空间) rg_real_error	1.44 Å
I(0) (实空间) i0_real	1.8170e+08
I(0) 误差 (实空间) i0_real_error	3.3240e+06
Rg (倒空间) rg_reciprocal	38.33 Å
I(0) (倒空间) i0_reciprocal	181700000.0000
解质量估计 total_estimate	0.6317
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	51.3 Å
偏度 Skewness skewness	0.417
峰度 Kurtosis kurtosis	-0.074
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22490000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.690; Stabil: 1.000; Sysdev: 0.132; Positv: 1.000; Valcen: 0.872; Smooth: 0.869

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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	DNA POLYMERASE III BETA SUBUNIT
分子量 formula_weight	40630.5 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	8485

MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL

来源 Source

来源生物 organism	ESCHERICHIA COLI
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	DNA POLYMERASE IV
分子量 formula_weight	13556.6 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	C,D

HHHHHHVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDPQMERQLVLGL

来源 Source

来源生物 organism	ESCHERICHIA COLI
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 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	947

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1unna1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.131 — DNA clamp
超家族 Superfamily superfamily	d.131.1 — DNA clamp
家族 Family family	d.131.1.1 — DNA polymerase III, beta subunit

结构域编号 domain_id	d1unna2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.131 — DNA clamp
超家族 Superfamily superfamily	d.131.1 — DNA clamp
家族 Family family	d.131.1.1 — DNA polymerase III, beta subunit

结构域编号 domain_id	d1unna3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.131 — DNA clamp
超家族 Superfamily superfamily	d.131.1 — DNA clamp
家族 Family family	d.131.1.1 — DNA polymerase III, beta subunit

结构域编号 domain_id	d1unnb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.131 — DNA clamp
超家族 Superfamily superfamily	d.131.1 — DNA clamp
家族 Family family	d.131.1.1 — DNA polymerase III, beta subunit

结构域编号 domain_id	d1unnb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.131 — DNA clamp
超家族 Superfamily superfamily	d.131.1 — DNA clamp
家族 Family family	d.131.1.1 — DNA polymerase III, beta subunit

结构域编号 domain_id	d1unnb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.131 — DNA clamp
超家族 Superfamily superfamily	d.131.1 — DNA clamp
家族 Family family	d.131.1.1 — DNA polymerase III, beta subunit

结构域编号 domain_id	d1unnc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.240 — Lesion bypass DNA polymerase (Y-family), little finger domain
超家族 Superfamily superfamily	d.240.1 — Lesion bypass DNA polymerase (Y-family), little finger domain
家族 Family family	d.240.1.1 — Lesion bypass DNA polymerase (Y-family), little finger domain

结构域编号 domain_id	d1unnc2
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	d1unnd1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.240 — Lesion bypass DNA polymerase (Y-family), little finger domain
超家族 Superfamily superfamily	d.240.1 — Lesion bypass DNA polymerase (Y-family), little finger domain
家族 Family family	d.240.1.1 — Lesion bypass DNA polymerase (Y-family), little finger domain

结构域编号 domain_id	d1unnd2
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 (8 domains)

结构域编号 domain_id	1unnA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	150 — DNA Polymerase III; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

结构域编号 domain_id	1unnA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	150 — DNA Polymerase III; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

结构域编号 domain_id	1unnA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	150 — DNA Polymerase III; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

结构域编号 domain_id	1unnB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	150 — DNA Polymerase III; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

结构域编号 domain_id	1unnB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	150 — DNA Polymerase III; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

结构域编号 domain_id	1unnB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	150 — DNA Polymerase III; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

结构域编号 domain_id	1unnC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	100 — DNA polymerase, Y-family, little finger domain

结构域编号 domain_id	1unnD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	100 — DNA polymerase, Y-family, little finger domain

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7. 引用文献 (1)

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晶胞边长 a length_a	146.451 Å
晶胞边长 b length_b	70.117 Å
晶胞边长 c length_c	110.916 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	8

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	62.100 Å
R 因子 r_factor	—
R_work r_work	0.1790
R_free r_free	0.2400

fit	/app/data/saxs_computation/un/1unn/1unn.fit
pddf	/app/data/pr_computation/un/1unn/1unn.pr.out
profile	/app/data/saxs_computation/un/1unn/1unn.dat

Complex of beta-clamp processivity factor and little finger domain of PolIV

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

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)