1ltl

THE DODECAMER STRUCTURE OF MCM FROM ARCHAEAL M. THERMOAUTOTROPHICUM

Method: X-RAY DIFFRACTION D_max: 187.6 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	1ltl
沉积日期 deposition_date	2002-05-20
结构标题 title	THE DODECAMER STRUCTURE OF MCM FROM ARCHAEAL M. THERMOAUTOTROPHICUM
关键词 keywords	replication; REPLICATION
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	53.80 Å
回转半径 Rg (电子) rg_electron	54.24 Å
零角强度 I(0) i0	404635000.00
分子量 molecular_weight	165630.0 kDa
排除体积 excluded_volume	207100 Å³
包络体积 envelope_volume	338030 Å³
水化壳体积 shell_volume	55226 Å³
包络直径 envelope_diameter	192.2 Å
壳层 Rg shell_rg	53.21 Å
包络 Rg envelope_rg	52.03 Å
形状 Rg shape_rg	54.24 Å
总 Rg total_rg	54.21 Å
总原子数 total_atoms	11633
残基数 n_residues	1437
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	187.6 Å
Rg (实空间) rg_real	54.10 Å
Rg 误差 (实空间) rg_real_error	1.92 Å
I(0) (实空间) i0_real	4.0460e+08
I(0) 误差 (实空间) i0_real_error	7.9190e+06
Rg (倒空间) rg_reciprocal	53.52 Å
I(0) (倒空间) i0_reciprocal	404300000.0000
解质量估计 total_estimate	0.6152
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	45.3 Å
偏度 Skewness skewness	0.374
峰度 Kurtosis kurtosis	-0.628
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	26050000.0000
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: 0.810; Stabil: 1.000; Sysdev: 0.001; Positv: 1.000; Valcen: 0.857; Smooth: 0.703

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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 (2)

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1ltla_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.11 — DNA replication initiator (cdc21/cdc54) N-terminal domain

结构域编号 domain_id	d1ltlb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.11 — DNA replication initiator (cdc21/cdc54) N-terminal domain

结构域编号 domain_id	d1ltlc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.11 — DNA replication initiator (cdc21/cdc54) N-terminal domain

结构域编号 domain_id	d1ltld_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.11 — DNA replication initiator (cdc21/cdc54) N-terminal domain

结构域编号 domain_id	d1ltle_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.11 — DNA replication initiator (cdc21/cdc54) N-terminal domain

结构域编号 domain_id	d1ltlf_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.11 — DNA replication initiator (cdc21/cdc54) N-terminal domain

CATH v4.4 (18 domains)

结构域编号 domain_id	1ltlA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1640 — mini-chromosome maintenance (MCM) complex, chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — mini-chromosome maintenance (MCM) complex, chain A, domain 1

结构域编号 domain_id	1ltlA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1ltlA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ltlB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1640 — mini-chromosome maintenance (MCM) complex, chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — mini-chromosome maintenance (MCM) complex, chain A, domain 1

结构域编号 domain_id	1ltlB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1ltlB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ltlC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1640 — mini-chromosome maintenance (MCM) complex, chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — mini-chromosome maintenance (MCM) complex, chain A, domain 1

结构域编号 domain_id	1ltlC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1ltlC03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ltlD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1640 — mini-chromosome maintenance (MCM) complex, chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — mini-chromosome maintenance (MCM) complex, chain A, domain 1

结构域编号 domain_id	1ltlD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1ltlD03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ltlE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1640 — mini-chromosome maintenance (MCM) complex, chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — mini-chromosome maintenance (MCM) complex, chain A, domain 1

结构域编号 domain_id	1ltlE02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1ltlE03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ltlF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1640 — mini-chromosome maintenance (MCM) complex, chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — mini-chromosome maintenance (MCM) complex, chain A, domain 1

结构域编号 domain_id	1ltlF02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1ltlF03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	28 — Rubrerythrin, domain 2
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	192.321 Å
晶胞边长 b length_b	192.321 Å
晶胞边长 c length_c	365.539 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	120.00 °
晶胞分子数 Z z_pdb	108

空间群 space_group	H 3 2
空间群编号 int_tables_number	155
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2450
R_free r_free	0.2950

描述 description	DNA replication initiator (Cdc21/Cdc54)
分子量 formula_weight	32336.7 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	11633

THE DODECAMER STRUCTURE OF MCM FROM ARCHAEAL M. THERMOAUTOTROPHICUM

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 non-polymer

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (6 domains)

CATH v4.4 (18 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Methanothermobacter thermautotrophicus
NCBI 分类编号 ncbi_taxonomy_id	145262
宿主生物 host_organism	Escherichia coli

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

fit	/app/data/saxs_computation/lt/1ltl/1ltl.fit
pddf	/app/data/pr_computation/lt/1ltl/1ltl.pr.out
profile	/app/data/saxs_computation/lt/1ltl/1ltl.dat