1jqj

;Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader Complex of E. coli DNA Polymerase III: Structure of the beta-delta complex ;

Method: X-RAY DIFFRACTION D_max: 165.7 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1jqj
沉积日期 deposition_date	2001-08-07
结构标题 title	;Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader Complex of E. coli DNA Polymerase III: Structure of the beta-delta complex ;
关键词 keywords	DNA Polymerase, Processivity Clamp, Clamp Loader, DNA Replication, AAA+ ATPase, TRANSFERASE; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	53.48 Å
回转半径 Rg (电子) rg_electron	53.91 Å
零角强度 I(0) i0	348825000.00
分子量 molecular_weight	154620.0 kDa
排除体积 excluded_volume	193740 Å³
包络体积 envelope_volume	320800 Å³
水化壳体积 shell_volume	51468 Å³
包络直径 envelope_diameter	176.2 Å
壳层 Rg shell_rg	53.08 Å
包络 Rg envelope_rg	52.63 Å
形状 Rg shape_rg	53.93 Å
总 Rg total_rg	53.85 Å
总原子数 total_atoms	10860
残基数 n_residues	1385
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	165.7 Å
Rg (实空间) rg_real	53.83 Å
Rg 误差 (实空间) rg_real_error	1.63 Å
I(0) (实空间) i0_real	3.4880e+08
I(0) 误差 (实空间) i0_real_error	7.1500e+06
Rg (倒空间) rg_reciprocal	53.15 Å
I(0) (倒空间) i0_reciprocal	348500000.0000
解质量估计 total_estimate	0.5877
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	51.4 Å
偏度 Skewness skewness	0.405
峰度 Kurtosis kurtosis	-0.647
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13540000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 0.999; Sysdev: 0.001; Positv: 1.000; Valcen: 0.928; Smooth: 0.001

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (2)

Entity 1 polymer

描述 description	DNA polymerase III, beta chain
分子量 formula_weight	40546.4 kDa
EC 编号 ec_number	2.7.7.7
突变 mutation	I272A, L273A
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	10860

MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAAASNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL

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 III, delta subunit
分子量 formula_weight	38745.6 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

MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLALAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEGSEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQAVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG

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

▼

6. 折叠分类 (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1jqja1
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	d1jqja2
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	d1jqja3
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	d1jqjb1
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	d1jqjb2
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	d1jqjb3
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	d1jqjc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.80 — post-AAA+ oligomerization domain-like
超家族 Superfamily superfamily	a.80.1 — post-AAA+ oligomerization domain-like
家族 Family family	a.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain

结构域编号 domain_id	d1jqjc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.20 — Extended AAA-ATPase domain

结构域编号 domain_id	d1jqjd1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.80 — post-AAA+ oligomerization domain-like
超家族 Superfamily superfamily	a.80.1 — post-AAA+ oligomerization domain-like
家族 Family family	a.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain

结构域编号 domain_id	d1jqjd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.20 — Extended AAA-ATPase domain

CATH v4.4 (12 domains)

结构域编号 domain_id	1jqjA01
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	1jqjA02
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	1jqjA03
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	1jqjB01
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	1jqjB02
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	1jqjB03
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	1jqjC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1jqjC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	272 — Zinc Finger, Delta Prime; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1jqjC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	1jqjD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1jqjD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	272 — Zinc Finger, Delta Prime; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1jqjD03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	60 —

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	198.836 Å
晶胞边长 b length_b	99.293 Å
晶胞边长 c length_c	113.023 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	119.17 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	500.000 Å
R 因子 r_factor	—
R_work r_work	0.2658
R_free r_free	0.3079

fit	/app/data/saxs_computation/jq/1jqj/1jqj.fit
pddf	/app/data/pr_computation/jq/1jqj/1jqj.pr.out
profile	/app/data/saxs_computation/jq/1jqj/1jqj.dat

;Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader Complex of E. coli DNA Polymerase III: Structure of the beta-delta complex ;

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)