PDB-1wb9: Crystal Structure of E. coli DNA Mismatch Repair enzyme MutS, E38...

ID or keywords:

Entry

Database: PDB / ID: 1wb9

Title

Crystal Structure of E. coli DNA Mismatch Repair enzyme MutS, E38T mutant, in complex with a G.T mismatch

Components

5'-D(*AP*CP*TP*GP*GP*TP*GP*CP*TP*TP *GP*GP*CP*AP*GP*CP*T)-3'
5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP *CP*AP*CP*CP*AP*GP*TP*G)-3'
DNA MISMATCH REPAIR PROTEIN MUTS

Keywords

DNA-BINDING / ATP-BINDING / DNA BINDING / DNA REPAIR / MISMATCH RECOGNITION

Function / homology

Function and homology information

adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding ...
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Natrajan, G. / Georgijevic, D. / Lebbink, J.H.G. / Winterwerp, H.H.K. / de Wind, N. / Sixma, T.K.

Citation

Journal: Embo J. / Year: 2006
Title: Dual Role of Muts Glutamate 38 in DNA Mismatch Discrimination and in the Authorization of Repair.
Authors: Lebbink, J.H.G. / Georgijevic, D. / Natrajan, G. / Fish, A. / Winterwerp, H.H.K. / Sixma, T.K. / De Wind, N.

History

Deposition	Oct 31, 2004	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 18, 2006	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1wb9.cif.gz	351.2 KB	Display	PDBx/mmCIF format
PDB format	pdb1wb9.ent.gz	279.9 KB	Display	PDB format
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Validation report

Summary document	1wb9_validation.pdf.gz	814.2 KB	Display	wwPDB validaton report
Full document	1wb9_full_validation.pdf.gz	839.9 KB	Display
Data in XML	1wb9_validation.xml.gz	64.6 KB	Display
Data in CIF	1wb9_validation.cif.gz	94.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wb/1wb9 ftp://data.pdbj.org/pub/pdb/validation_reports/wb/1wb9	HTTPS FTP

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Related structure data

Related structure data	1wbbC 1wbdC 1e3mS 1ng9 1oh5 1oh6 1oh7 1oh8 1w7a S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1oh7-d 1wbb-d 1w7a-d 2wtu-d 1e3m-d 1wbd-d 1oh8-d 1ng9-d 3zlj-1 3k0s-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: DNA MISMATCH REPAIR PROTEIN MUTS

B: DNA MISMATCH REPAIR PROTEIN MUTS

E: 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP *CP*AP*CP*CP*AP*GP*TP*G)-3'

F: 5'-D(*AP*CP*TP*GP*GP*TP*GP*CP*TP*TP *GP*GP*CP*AP*GP*CP*T)-3'

hetero molecules

190 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	89.650, 92.116, 260.744
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	DNA MISMATCH REPAIR PROTEIN MUTS Mass: 89576.352 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-800 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PM800 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (BL21) / Variant (production host): PLYSS / References: UniProt: P23909

#1: Protein

DNA MISMATCH REPAIR PROTEIN MUTS

Mass: 89576.352 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-800 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

ESCHERICHIA COLI (E. coli) / Plasmid: PM800 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (BL21) / Variant (production host): PLYSS / References: UniProt: P23909

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DNA chain , 2 types, 2 molecules EF

#2: DNA chain	5'-D(APGPCPTPGPCPCPAPGPGP CPAPCPCPAPGPTPG)-3' Mass: 5526.581 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: G\:T MISMATCH DNA
#3: DNA chain	5'-D(APCPTPGPGPTPGPCPTPTP GPGPCPAPGPCPT)-3' Mass: 5234.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI* (E. coli)

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Non-polymers , 3 types, 957 molecules

#4: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 955 / Source method: isolated from a natural source / Formula: H₂O

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Details

Compound details	ENGINEERED RESIDUES CHAINS A AND B, GLU 38 THR

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 56.2 %
Crystal grow	pH: 7.5 Details: 25 MM HEPES(7.5), 300 MM NACL, 10 MM MGCL2, 14 % PEG 6000., pH 7.50

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
Detector	Type: ADSC CCD / Detector: CCD / Date: Mar 1, 2002 / Details: TOROIDAL MIRROR
Radiation	Monochromator: DIAMOND (111) GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.934 Å / Relative weight: 1
Reflection	Resolution: 2.1→25 Å / Num. obs: 121248 / % possible obs: 91.7 % / Redundancy: 3.05 % / B_iso Wilson estimate: 31.65 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 14.46
Reflection shell	Resolution: 2.1→2.15 Å / Redundancy: 1.88 % / R_merge(I) obs: 0.49 / Mean I/σ(I) obs: 1.52 / % possible all: 47

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E3M

1e3m

Resolution: 2.1→20 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.927 / SU B: 5.398 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.234	2306	2.04 %	AS FOR ENTRY 1E3M
R_work	0.189	-	-	-
obs	0.19	113368	91.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 18.14 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.288 Å²	0 Å²	0 Å²
2-	-	2.323 Å²	0 Å²
3-	-	-	-1.034 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12165	714	28	955	13862

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.021	13204
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	11957
X-RAY DIFFRACTION	r_angle_refined_deg	1.421	2.044	18022
X-RAY DIFFRACTION	r_angle_other_deg	0.861	3	27742
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.017	5	1536
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	2014
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	14134
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2512
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	2688
X-RAY DIFFRACTION	r_nbd_other	0.236	0.2	14054
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	7722
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.176	0.2	768
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.183	0.2	34
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.255	0.2	134
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.198	0.2	35
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.596	1.5	7674
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.124	2	12329
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.877	3	5530
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.07	4.5	5693
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.15 Å / Total num. of bins used: 10 /

	R_factor	Num. reflection
R_free	0.299	119
R_work	0.259	6156

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	3.443	-0.0123	0.9831	2.4695	0.3655	3.2297	0.0493	-0.053	0.0356	-0.0466	0.0181	0.0809	-0.1341	-0.0446	-0.0674	0.1882	-0.0218	0.022	0.1953	0.0234	0.1175	95.924	81.863	33.81
2	2.2754	0.3702	-0.0884	1.6635	0.0677	1.4327	0.1018	0.0378	-0.0022	-0.071	-0.0344	0.0409	0.0211	0.0299	-0.0675	0.0917	0.0123	-0.0041	0.1039	0.0119	0.1105	121.626	82.988	18.903
3	0.9845	-0.4239	-0.7544	0.9408	0.7422	2.1151	0.0032	-0.266	-0.1652	0.1467	0.0541	-0.1065	0.1102	0.0998	-0.0573	0.1575	-0.009	-0.038	0.2261	0.048	0.2003	135.283	70.675	32.819
4	2.9833	-3.1831	-1.8086	6.7081	3.5709	3.5927	-0.17	-0.2865	-0.1304	0.2582	0.2269	-0.3152	0.352	0.2942	-0.0569	0.1509	0.0247	-0.0633	0.2607	0.0677	0.1605	142.962	63.538	32.116
5	3.0145	0.8063	-0.9428	4.0035	0.0992	11.0188	-0.0765	0.0052	-0.0201	0.0731	0.253	-0.1026	-0.0437	0.4791	-0.1766	0.257	0.0296	0.0168	0.2276	-0.03	0.1116	92.489	75.388	76.784
6	5.2084	-0.4717	-3.6254	1.37	0.8892	3.5662	0.1066	-0.8821	0.2253	0.3519	0.1142	0.0527	0.0116	0.417	-0.2208	0.3231	-0.0205	-0.0556	0.4635	0.0116	0.1953	126.448	82.93	54.07
7	3.7574	-0.1159	-3.5334	0.1161	-0.0851	2.5846	0.3476	-0.2088	0.3929	0.203	-0.0515	0.0798	-0.3036	0.0094	-0.2961	0.3185	-0.0731	0.0339	0.4967	-0.0746	0.2537	116.461	87.292	54.825
8	0.7584	0.2178	0.5375	0.9541	0.9186	1.9815	0.0403	-0.048	-0.0426	0.0241	-0.0233	-0.0899	0.0733	-0.0743	-0.0171	0.11	-0.0079	0.0207	0.098	0.0126	0.2313	140.514	57.892	5.348
9	3.4425	1.6564	-1.9761	6.6031	-4.1782	8.9196	-0.1086	-0.1251	-0.8262	0.197	0.1646	-0.2919	0.9478	0.0394	-0.056	0.2442	0.0172	-0.0134	0.1216	-0.0365	0.4392	143.913	40.852	5.775
10	5.5303	1.9421	-0.886	4.7419	-1.2508	6.2705	-0.0775	-0.0134	-0.4038	0.1268	0.1076	-0.4148	-0.0378	-0.0152	-0.0301	0.1057	0.0879	-0.0421	0.0801	0.0051	0.247	133.784	32.29	-5.079
11	5.6351	2.1875	-0.1032	4.7843	0.7525	6.3486	0.4604	-0.6507	0.4664	0.7021	-0.3256	-0.3356	-0.8577	0.7857	-0.1348	0.5745	-0.2291	0.0551	0.5022	-0.0432	0.3651	106.169	48.088	43.522
12	2.0866	0.2465	-0.0309	2.9677	0.7253	2.6214	0.1158	-0.0527	-0.1161	-0.0131	0.0088	-0.3641	0.155	0.3193	-0.1246	0.1913	0.0066	0.0021	0.197	0.024	0.1377	101.776	27.358	25.902
13	1.7529	-0.0958	-1.5752	0.6231	0.099	2.2427	0.1079	-0.0074	0.0627	0.0311	-0.0435	-0.0042	-0.175	-0.0326	-0.0644	0.1754	0.0304	0.0094	0.147	0.0527	0.1587	87.255	40.592	13.597
14	0.0149	1.0626	-3.0301	2.9958	-4.6293	12.6012	0.0098	-0.0263	0.1764	-0.0518	0.1202	0.1571	-0.1938	-0.6084	-0.13	0.0827	0.0791	0.0045	0.1702	0.0599	0.1243	85.584	43.585	3.744
15	4.8544	2.1893	0.8886	7.1232	2.0458	1.9298	0.0155	0.0079	0.0591	-0.0759	-0.3007	0.5912	-0.1273	-0.3598	0.2851	0.3622	0.0541	-0.0021	0.4851	-0.0509	0.194	72.34	73.518	61.539
16	1.0074	-0.8101	-0.8204	3.4324	4.5403	7.4	0.0746	-0.131	0.0397	0.0661	-0.188	0.1406	-0.0983	-0.5152	0.1134	0.2526	0.0167	0.0294	0.3124	0.0456	0.2454	70.408	44.048	33.461
17	0.8012	-0.7099	-0.5065	1.6852	1.2648	1.0026	-0.0844	-0.3802	0.0099	0.5294	-0.0488	0.1552	0.3425	0.0592	0.1332	0.3264	-0.0769	0.0556	0.3892	0.022	0.2069	73.459	44.6	43.718
18	5.2922	-0.2187	-0.6669	0.2621	-0.199	0.7501	0.0069	0.0045	-0.1262	-0.0383	0.0298	-0.0467	-0.0136	-0.0145	-0.0367	0.1261	0.0078	0.0104	0.0535	0.0202	0.1418	110.284	37.624	-6.887
19	2.5349	1.3557	-0.0817	20.2115	0.236	-0.4847	-0.1394	0.2069	0.6117	0.1376	0.2127	0.5514	-0.1287	-0.1166	-0.0733	0.2062	0.0104	0.0309	0.2036	0.0366	0.2085	112.134	52.352	-16.381
20	4.123	1.5201	0.4974	4.9395	3.0496	4.2809	-0.1481	0.0959	0.2453	-0.4007	0.1999	-0.1477	-0.1759	0.1877	-0.0518	0.1438	0.0104	0.0402	0.1196	0.0686	0.1337	129.208	57.572	-16.203
21	1.7453	0.9689	-0.7756	2.3236	-1.6538	5.8009	-0.0885	-0.0194	0.1019	0.3458	0.1522	0.4739	-0.1033	-0.5026	-0.0637	0.3422	-0.05	0.0398	0.3536	0.0175	0.2234	85.424	77.391	50.931

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 115
2	X-RAY DIFFRACTION	2	A	116 - 265
3	X-RAY DIFFRACTION	3	A	266 - 387
4	X-RAY DIFFRACTION	4	A	550 - 567
5	X-RAY DIFFRACTION	5	A	444 - 503
6	X-RAY DIFFRACTION	6	A	388 - 443
7	X-RAY DIFFRACTION	7	A	504 - 549
8	X-RAY DIFFRACTION	8	A	568 - 741
9	X-RAY DIFFRACTION	8	A	1801
10	X-RAY DIFFRACTION	8	A	1802
11	X-RAY DIFFRACTION	9	A	742 - 765
12	X-RAY DIFFRACTION	10	A	766 - 800
13	X-RAY DIFFRACTION	11	B	14 - 115
14	X-RAY DIFFRACTION	12	B	116 - 265
15	X-RAY DIFFRACTION	13	B	266 - 387
16	X-RAY DIFFRACTION	14	B	550 - 567
17	X-RAY DIFFRACTION	15	B	444 - 503
18	X-RAY DIFFRACTION	16	B	388 - 443
19	X-RAY DIFFRACTION	17	B	504 - 549
20	X-RAY DIFFRACTION	18	B	568 - 741
21	X-RAY DIFFRACTION	19	B	742 - 765
22	X-RAY DIFFRACTION	20	B	766 - 800
23	X-RAY DIFFRACTION	21	E	1 - 18
24	X-RAY DIFFRACTION	21	F	14 - 30

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