1ksx

Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex

Method: X-RAY DIFFRACTION D_max: 112.3 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	1ksx
沉积日期 deposition_date	2002-01-14
结构标题 title	Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex
关键词 keywords	PAPILLOMAVIRUS, DNA-BINDING DOMAIN, REPLICATION, INITIATOR PROTEIN, HELICASE, REPLICATION-DNA COMPLEX; 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	36.05 Å
回转半径 Rg (电子) rg_electron	35.76 Å
零角强度 I(0) i0	434585000.00
分子量 molecular_weight	158290.0 kDa
排除体积 excluded_volume	193680 Å³
包络体积 envelope_volume	265020 Å³
水化壳体积 shell_volume	59912 Å³
包络直径 envelope_diameter	124.7 Å
壳层 Rg shell_rg	43.79 Å
包络 Rg envelope_rg	34.88 Å
形状 Rg shape_rg	35.78 Å
总 Rg total_rg	36.22 Å
总原子数 total_atoms	11024
残基数 n_residues	1244
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	112.3 Å
Rg (实空间) rg_real	35.80 Å
Rg 误差 (实空间) rg_real_error	0.72 Å
I(0) (实空间) i0_real	4.3460e+08
I(0) 误差 (实空间) i0_real_error	6.8690e+06
Rg (倒空间) rg_reciprocal	35.96 Å
I(0) (倒空间) i0_reciprocal	434600000.0000
解质量估计 total_estimate	0.8965
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	46.0 Å
偏度 Skewness skewness	0.079
峰度 Kurtosis kurtosis	-0.478
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	40500000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.975

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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 (3)

Entity 1 polymer

描述 description	E1 Recognition Sequence
分子量 formula_weight	6444.2 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	C,G,K,O
原子数 atom_count	11044

ATAATTGTTGTTAACAACAAT

Entity 2 polymer

描述 description	REPLICATION PROTEIN E1
分子量 formula_weight	16877.8 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,E,F,I,J,M,N

GSRATVFKLGLFKSLFLCSFHDITRLFKNDKTTNQQWVLAVFGLAEVFFEASFELLKKQCSFLQMQKRSHEGGTCAVYLICFNTAKSRETVRNLMANMLNVREECLMLQPPKIRGLSAALFWFKSSLSPATLKHGALPEWIRAQTTLN

来源 Source

来源生物 organism	Bovine papillomavirus
NCBI 分类编号 ncbi_taxonomy_id	10571
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 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	20

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1ksxa_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.89 — Origin of replication-binding domain, RBD-like
超家族 Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
家族 Family family	d.89.1.2 — Replication initiation protein E1

结构域编号 domain_id	d1ksxb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.89 — Origin of replication-binding domain, RBD-like
超家族 Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
家族 Family family	d.89.1.2 — Replication initiation protein E1

结构域编号 domain_id	d1ksxe_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.89 — Origin of replication-binding domain, RBD-like
超家族 Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
家族 Family family	d.89.1.2 — Replication initiation protein E1

结构域编号 domain_id	d1ksxf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.89 — Origin of replication-binding domain, RBD-like
超家族 Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
家族 Family family	d.89.1.2 — Replication initiation protein E1

结构域编号 domain_id	d1ksxi_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.89 — Origin of replication-binding domain, RBD-like
超家族 Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
家族 Family family	d.89.1.2 — Replication initiation protein E1

结构域编号 domain_id	d1ksxj_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.89 — Origin of replication-binding domain, RBD-like
超家族 Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
家族 Family family	d.89.1.2 — Replication initiation protein E1

结构域编号 domain_id	d1ksxm_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.89 — Origin of replication-binding domain, RBD-like
超家族 Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
家族 Family family	d.89.1.2 — Replication initiation protein E1

结构域编号 domain_id	d1ksxn_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.89 — Origin of replication-binding domain, RBD-like
超家族 Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
家族 Family family	d.89.1.2 — Replication initiation protein E1

CATH v4.4 (8 domains)

结构域编号 domain_id	1ksxA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1310 — Replication Protein E1; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ksxB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1310 — Replication Protein E1; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ksxE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1310 — Replication Protein E1; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ksxF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1310 — Replication Protein E1; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ksxI00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1310 — Replication Protein E1; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ksxJ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1310 — Replication Protein E1; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ksxM00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1310 — Replication Protein E1; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ksxN00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1310 — Replication Protein E1; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	84.246 Å
晶胞边长 b length_b	103.650 Å
晶胞边长 c length_c	124.996 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	99.53 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	3.200 Å
最低分辨率 resolution_low	42.620 Å
R 因子 r_factor	—
R_work r_work	0.2630
R_free r_free	0.2850

fit	/app/data/saxs_computation/ks/1ksx/1ksx.fit
pddf	/app/data/pr_computation/ks/1ksx/1ksx.pr.out
profile	/app/data/saxs_computation/ks/1ksx/1ksx.dat

Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation 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 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)