1nne

Crystal Structure of the MutS-ADPBeF3-DNA complex

Method: X-RAY DIFFRACTION D_max: 130.5 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	1nne
沉积日期 deposition_date	2003-01-13
结构标题 title	Crystal Structure of the MutS-ADPBeF3-DNA complex
关键词 keywords	DNA, DNA BINDING PROTEIN-DNA COMPLEX; DNA BINDING PROTEIN/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	41.07 Å
回转半径 Rg (电子) rg_electron	40.19 Å
零角强度 I(0) i0	554067000.00
分子量 molecular_weight	185030.0 kDa
排除体积 excluded_volume	228610 Å³
包络体积 envelope_volume	319740 Å³
水化壳体积 shell_volume	64894 Å³
包络直径 envelope_diameter	135.0 Å
壳层 Rg shell_rg	47.40 Å
包络 Rg envelope_rg	38.95 Å
形状 Rg shape_rg	40.19 Å
总 Rg total_rg	40.60 Å
总原子数 total_atoms	12990
残基数 n_residues	1563
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	130.5 Å
Rg (实空间) rg_real	40.95 Å
Rg 误差 (实空间) rg_real_error	0.94 Å
I(0) (实空间) i0_real	5.5410e+08
I(0) 误差 (实空间) i0_real_error	1.0250e+07
Rg (倒空间) rg_reciprocal	41.07 Å
I(0) (倒空间) i0_reciprocal	554100000.0000
解质量估计 total_estimate	0.6697
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	51.5 Å
偏度 Skewness skewness	0.185
峰度 Kurtosis kurtosis	-0.512
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	45560000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 0.008; Positv: 1.000; Valcen: 0.991; 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 (8)

Entity 1 polymer

描述 description	5'-D(GPCPGPAPCPGPCPTPAPGPCPGPTPGPCPGPGPCPTPCPGPTP*C)-3'
分子量 formula_weight	7074.5 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	C
原子数 atom_count	13089

GCGACGCTAGCGTGCGGCTCGTC

Entity 2 polymer

描述 description	5'-D(PGPGPAPCPGPAPGPCPCPGPCPCPGPCPTPAPGPCPGPTPCPG)-3'
分子量 formula_weight	6779.4 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	D

GGACGAGCCGCCGCTAGCGTCG

Entity 3 polymer

描述 description	DNA Mismatch Repair protein MutS
分子量 formula_weight	85776.5 kDa
来源方法 src_method	nat
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

MEGMLKGEGPGPLPPLLQQYVELRDQYPDYLLLFQVGDFYECFGEDAERLARALGLVLTHKTSKDFTTPMAGIPLRAFEAYAERLLKMGFRLAVADQVEPAEEAEGLVRREVTQLLTPGTLLQESLLPREANYLAAIATGDGWGLAFLDVSTGEFKGTVLKSKSALYDELFRHRPAEVLLAPELLENGAFLDEFRKRFPVMLSEAPFEPEGEGPLALRRARGALLAYAQRTQGGALSLQPFRFYDPGAFMRLPEATLRALEVFEPLRGQDTLFSVLDETRTAPGRRLLQSWLRHPLLDRGPLEARLDRVEGFVREGALREGVRRLLYRLADLERLATRLELGRASPKDLGALRRSLQILPELRALLGEEVGLPDLSPLKEELEAALVEDPPLKVSEGGLIREGYDPDLDALRAAHREGVAYFLELEERERERTGIPTLKVGYNAVFGYYLEVTRPYYERVPKEYRPVQTLKDRQRYTLPEMKEKEREVYRLEALIRRREEEVFLEVRERAKRQAEALREAARILAELDVYAALAEVAVRYGYVRPRFGDRLQIRAGRHPVVERRTEFVPNDLEMAHELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKEATENSLVLLDEVGRGTSSLDGVAIATAVAEALHERRAYTLFATHYFELTALGLPRLKNLHVAAREEAGGLVFYHQVLPGPASKSYGVEVAAMAGLPKEVVARARALLQAMAAR

Entity 4 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 5 non-polymer

描述 description	BERYLLIUM TRIFLUORIDE ION
分子量 formula_weight	66.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 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	99

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1nnea1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.113 — DNA repair protein MutS, domain III
超家族 Superfamily superfamily	a.113.1 — DNA repair protein MutS, domain III
家族 Family family	a.113.1.1 — DNA repair protein MutS, domain III

结构域编号 domain_id	d1nnea2
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.37.1.12 — ABC transporter ATPase domain-like

结构域编号 domain_id	d1nnea3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.6 — DNA repair protein MutS, domain II
家族 Family family	c.55.6.1 — DNA repair protein MutS, domain II

结构域编号 domain_id	d1nnea4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.75 — MutS N-terminal domain-like
超家族 Superfamily superfamily	d.75.2 — DNA repair protein MutS, domain I
家族 Family family	d.75.2.1 — DNA repair protein MutS, domain I

结构域编号 domain_id	d1nneb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.113 — DNA repair protein MutS, domain III
超家族 Superfamily superfamily	a.113.1 — DNA repair protein MutS, domain III
家族 Family family	a.113.1.1 — DNA repair protein MutS, domain III

结构域编号 domain_id	d1nneb2
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.37.1.12 — ABC transporter ATPase domain-like

结构域编号 domain_id	d1nneb3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.6 — DNA repair protein MutS, domain II
家族 Family family	c.55.6.1 — DNA repair protein MutS, domain II

结构域编号 domain_id	d1nneb4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.75 — MutS N-terminal domain-like
超家族 Superfamily superfamily	d.75.2 — DNA repair protein MutS, domain I
家族 Family family	d.75.2.1 — DNA repair protein MutS, domain I

CATH v4.4 (10 domains)

结构域编号 domain_id	1nneA01
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	10 — DNA repair protein MutS, domain I

结构域编号 domain_id	1nneA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	110 — MutS, connector domain

结构域编号 domain_id	1nneA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1420 — MutS, DNA mismatch repair protein; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1nneA04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1420 — MutS, DNA mismatch repair protein; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1nneA05
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	1nneB01
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	10 — DNA repair protein MutS, domain I

结构域编号 domain_id	1nneB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	110 — MutS, connector domain

结构域编号 domain_id	1nneB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1420 — MutS, DNA mismatch repair protein; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1nneB04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1420 — MutS, DNA mismatch repair protein; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1nneB05
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

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7. 引用文献 (1)

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晶胞边长 a length_a	103.442 Å
晶胞边长 b length_b	113.224 Å
晶胞边长 c length_c	160.284 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 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	3.110 Å
最低分辨率 resolution_low	19.940 Å
R 因子 r_factor	0.2090
R_work r_work	0.2090
R_free r_free	0.2590

fit	/app/data/saxs_computation/nn/1nne/1nne.fit
pddf	/app/data/pr_computation/nn/1nne/1nne.pr.out
profile	/app/data/saxs_computation/nn/1nne/1nne.dat

Crystal Structure of the MutS-ADPBeF3-DNA 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 (8)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)