SAXSdb — 2j6u

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2j6u
沉积日期 deposition_date	2006-10-04
结构标题 title	Ternary complex of Sulfolobus solfataricus Dpo4 DNA polymerase, O6- methylguanine modified DNA, and dGTP.
关键词 keywords	;TRANSFERASE/DNA, TRANSFERASE-DNA COMPLEX, MUTATOR PROTEIN, DNA REPLICATION, O6-METHYLGUANINE, TRANSFERASE, METAL-BINDING, DNA POLYMERASE, TRANSLESION DNA SYNTHESIS, DNA-DIRECTED DNA POLYMERASE, DPO4, MAGNESIUM, DNA REPAIR, DNA DAMAGE, DNA-BINDING, NUCLEOTIDYLTRANSFERASE, SULFOLOBUS SOLFATARICUS ;; 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	23.61 Å
回转半径 Rg (电子) rg_electron	22.91 Å
零角强度 I(0) i0	48875600.00
分子量 molecular_weight	49480.0 kDa
排除体积 excluded_volume	59940 Å³
包络体积 envelope_volume	74140 Å³
水化壳体积 shell_volume	26719 Å³
包络直径 envelope_diameter	75.6 Å
壳层 Rg shell_rg	29.99 Å
包络 Rg envelope_rg	22.87 Å
形状 Rg shape_rg	22.92 Å
总 Rg total_rg	23.63 Å
总原子数 total_atoms	3437
残基数 n_residues	375
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	73.2 Å
Rg (实空间) rg_real	23.49 Å
Rg 误差 (实空间) rg_real_error	0.39 Å
I(0) (实空间) i0_real	4.8880e+07
I(0) 误差 (实空间) i0_real_error	5.7240e+05
Rg (倒空间) rg_reciprocal	23.52 Å
I(0) (倒空间) i0_reciprocal	48880000.0000
解质量估计 total_estimate	0.7126
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	29.8 Å
偏度 Skewness skewness	0.175
峰度 Kurtosis kurtosis	-0.480
角度范围 angular_range	— – 0.3350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7988000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 0.154; Positv: 1.000; Valcen: 0.998; Smooth: 0.985

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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 (6)

Entity 1 polymer

描述 description	DNA POLYMERASE IV
分子量 formula_weight	41086.8 kDa
EC 编号 ec_number	2.7.7.7
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	3624

HHHHHHMIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIEAIGLDKFFDT

来源 Source

来源生物 organism	SULFOLOBUS SOLFATARICUS
NCBI 分类编号 ncbi_taxonomy_id	273057
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	;5'-D(GPGPGPGPGPAPAPGPGPAP TPTPCPT)-3' ;
分子量 formula_weight	4400.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	P

GGGGGAAGGATTCT

Entity 3 polymer

描述 description	;5'-D(TPCPAPC G32PGPAPAPTPCPCP TPTPCPCPCPCP*C)-3' ;
分子量 formula_weight	5386.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	T

TCACGGAATCCTTCCCCC

Entity 4 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	3

Entity 5 non-polymer

描述 description	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 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	147

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d2j6ua1
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.240.1.0 — automated matches

结构域编号 domain_id	d2j6ua2
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.8.1.7 — Lesion bypass DNA polymerase (Y-family), catalytic domain

结构域编号 domain_id	d2j6ua3
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 (4 domains)

结构域编号 domain_id	2j6uA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

结构域编号 domain_id	2j6uA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	2j6uA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

结构域编号 domain_id	2j6uA04
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	92.318 Å
晶胞边长 b length_b	102.285 Å
晶胞边长 c length_c	52.485 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	4

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	2.500 Å
最低分辨率 resolution_low	28.690 Å
R 因子 r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2650

fit	/app/data/saxs_computation/j6/2j6u/2j6u.fit
pddf	/app/data/pr_computation/j6/2j6u/2j6u.pr.out
profile	/app/data/saxs_computation/j6/2j6u/2j6u.dat

Ternary complex of Sulfolobus solfataricus Dpo4 DNA polymerase, O6- methylguanine modified DNA, and dGTP.

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 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)