1wbd

Crystal structure of E. coli DNA mismatch repair enzyme MutS, E38Q mutant, in complex with a G.T mismatch

Method: X-RAY DIFFRACTION D_max: 130.6 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	1wbd
沉积日期 deposition_date	2004-10-31
结构标题 title	Crystal structure of E. coli DNA mismatch repair enzyme MutS, E38Q mutant, in complex with a G.T mismatch
关键词 keywords	DNA-BINDING, ATP-BINDING, DNA BINDING, DNA REPAIR, MISMATCH RECOGNITION; DNA-BINDING
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	40.86 Å
回转半径 Rg (电子) rg_electron	40.21 Å
零角强度 I(0) i0	554493000.00
分子量 molecular_weight	184370.0 kDa
排除体积 excluded_volume	227550 Å³
包络体积 envelope_volume	323260 Å³
水化壳体积 shell_volume	65308 Å³
包络直径 envelope_diameter	130.1 Å
壳层 Rg shell_rg	47.74 Å
包络 Rg envelope_rg	39.02 Å
形状 Rg shape_rg	40.22 Å
总 Rg total_rg	40.58 Å
总原子数 total_atoms	12913
残基数 n_residues	1577
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	130.6 Å
Rg (实空间) rg_real	40.71 Å
Rg 误差 (实空间) rg_real_error	0.86 Å
I(0) (实空间) i0_real	5.5450e+08
I(0) 误差 (实空间) i0_real_error	9.3120e+06
Rg (倒空间) rg_reciprocal	40.86 Å
I(0) (倒空间) i0_reciprocal	554600000.0000
解质量估计 total_estimate	0.8296
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	53.6 Å
偏度 Skewness skewness	0.142
峰度 Kurtosis kurtosis	-0.532
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	47870000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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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 MISMATCH REPAIR PROTEIN MUTS
分子量 formula_weight	89603.4 kDa
突变 mutation	YES
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	13160

MSAIENFDAHTPMMQQYLRLKAQHPEILLFYRMGDFYQLFYDDAKRASQLLDISLTKRGASAGEPIPMAGIPYHAVENYLAKLVNQGESVAICEQIGDPATSKGPVERKVVRIVTPGTISDEALLQERQDNLLAAIWQDSKGFGYATLDISSGRFRLSEPADRETMAAELQRTNPAELLYAEDFAEMSLIEGRRGLRRRPLWEFEIDTARQQLNLQFGTRDLVGFGVENAPRGLCAAGCLLQYAKDTQRTTLPHIRSITMEREQDSIIMDAATRRNLEITQNLAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRDTRVLLERQQTIGALQDFTAGLQPVLRQVGDLERILARLALRTARPRDLARMRHAFQQLPELRAQLETVDSAPVQALREKMGEFAELRDLLERAIIDTPPVLVRDGGVIASGYNEELDEWRALADGATDYLERLEVRERERTGLDTLKVGFNAVHGYYIQISRGQSHLAPINYMRRQTLKNAERYIIPELKEYEDKVLTSKGKALALEKQLYEELFDLLLPHLEALQQSASALAELDVLVNLAERAYTLNYTCPTFIDKPGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEHGDTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIKRARQKLRELESIS

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	;5'-D(APGPCPTPGPCPCPAPGPGP CPAPCPCPAPGPTPG)-3' ;
分子量 formula_weight	5526.6 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	E

AGCTGCCAGGCACCAGTG

Entity 3 polymer

描述 description	;5'-D(APCPTPGPGPTPGPCPTPTP GPGPCPAPGPCP*T)-3' ;
分子量 formula_weight	5234.4 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	F

ACTGGTGCTTGGCAGCT

Entity 4 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	1

Entity 5 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 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	247

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6. 折叠分类 (SCOP + CATH) 17 domains

SCOP 2.08 (7 domains)

结构域编号 domain_id	d1wbda1
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.113.1.0 — automated matches

结构域编号 domain_id	d1wbda2
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.37.1.0 — automated matches

结构域编号 domain_id	d1wbda3
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.55.6.0 — automated matches

结构域编号 domain_id	d1wbda4
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.75.2.0 — automated matches

结构域编号 domain_id	d1wbdb1
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.55.6.0 — automated matches

结构域编号 domain_id	d1wbdb2
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.113.1.0 — automated matches

结构域编号 domain_id	d1wbdb3
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.37.1.0 — automated matches

CATH v4.4 (10 domains)

结构域编号 domain_id	1wbdA01
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	1wbdA02
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	1wbdA03
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	1wbdA04
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	1wbdA05
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	1wbdB01
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	1wbdB02
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	1wbdB03
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	1wbdB04
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	1wbdB05
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	89.620 Å
晶胞边长 b length_b	92.042 Å
晶胞边长 c length_c	260.977 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	2.400 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2130
R_work r_work	0.2120
R_free r_free	0.2590

fit	/app/data/saxs_computation/wb/1wbd/1wbd.fit
pddf	/app/data/pr_computation/wb/1wbd/1wbd.pr.out
profile	/app/data/saxs_computation/wb/1wbd/1wbd.dat

Crystal structure of E. coli DNA mismatch repair enzyme MutS, E38Q mutant, in complex with a G.T mismatch

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) 17 domains

SCOP 2.08 (7 domains)

CATH v4.4 (10 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)