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- PDB-5yk4: Mismatch Repair Protein -

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Basic information

Entry
Database: PDB / ID: 5yk4
TitleMismatch Repair Protein
ComponentsDNA mismatch repair protein MutS
KeywordsDNA BINDING PROTEIN / MutS / Mismatch sensor / ATPase
Function / homology
Function and homology information


mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / damaged DNA binding / ATP binding
Similarity search - Function
DNA repair protein MutS, domain I / MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / DNA mismatch repair protein MutS / DNA mismatch repair protein MutS/MSH / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal / MutS, connector domain superfamily ...DNA repair protein MutS, domain I / MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / DNA mismatch repair protein MutS / DNA mismatch repair protein MutS/MSH / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal / MutS, connector domain superfamily / MutS domain I / MutS domain II / MutS family domain IV / MutS domain III / DNA mismatch repair MutS family / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core / DNA mismatch repair protein MutS, core domain superfamily / MutS domain V / DNA mismatch repair proteins mutS family signature. / DNA-binding domain of DNA mismatch repair MUTS family / ATPase domain of DNA mismatch repair MUTS family / MutS, DNA mismatch repair protein, domain I / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsNirwal, S. / Nair, D.T.
Funding support India, 1items
OrganizationGrant numberCountry
Department of BiotechnologyBT/PR882/BRB/10/935/2011 India
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Mechanism of formation of a toroid around DNA by the mismatch sensor protein.
Authors: Nirwal, S. / Kulkarni, D.S. / Sharma, A. / Rao, D.N. / Nair, D.T.
History
DepositionOct 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Sep 5, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA mismatch repair protein MutS
B: DNA mismatch repair protein MutS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,0544
Polymers180,2002
Non-polymers8542
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-37 kcal/mol
Surface area70040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.940, 102.400, 236.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein DNA mismatch repair protein MutS /


Mass: 90099.852 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-814
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria)
Strain: ATCC 700825 / FA 1090 / Gene: mutS, NGO1930 / Plasmid: PGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3 / References: UniProt: Q5F5J4
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.43 % / Description: FLAT RECTANGLES
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10-14% (W/V) PEG 4000, 0.1-0.2M MGCL2, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.97→50 Å / Num. obs: 43285 / % possible obs: 98.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 8.6
Reflection shellResolution: 2.97→3.05 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E3M

1e3m


Resolution: 2.97→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.904 / SU B: 42.556 / SU ML: 0.382 / Cross valid method: THROUGHOUT / ESU R Free: 0.429
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2301 5 %RANDOM
Rwork0.246 ---
obs0.247 43285 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 99.33 Å2
Baniso -1Baniso -2Baniso -3
1-3.63 Å20 Å20 Å2
2--0.57 Å20 Å2
3----4.2 Å2
Refinement stepCycle: LAST / Resolution: 2.97→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11810 0 54 119 11983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01912088
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0841.96916400
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14751533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.63424.117532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.812152041
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6011579
X-RAY DIFFRACTIONr_chiral_restr0.0590.21895
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219070
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5245.2976147
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.47.9437675
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.895.5125941
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined14.26349.54750319
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.97→3.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 190 -
Rwork0.34 3115 -
obs--99.88 %
Refinement TLS params.

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

IDL11 (°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)
11.7732-0.3352-1.59560.11570.21262.24160.04060.0274-0.1029-0.11570.0279-0.0449-0.0134-0.0163-0.06840.3791-0.01940.0390.56170.00330.46343.8275-3.4131-11.8828
20.3484-0.21390.61471.0479-0.09471.8854-0.033-0.0551-0.0485-0.2771-0.0131-0.0335-0.1346-0.24790.04610.46660.00430.00410.5486-0.00380.424915.188911.376-34.6943
30.41530.31530.28212.34330.65270.32370.0791-0.08950.0308-0.8244-0.0724-0.2681-0.08820.0743-0.00670.76110.07460.18650.48870.05130.393836.2463-10.6219-53.3766
40.6875-0.2343-1.0340.27810.30542.5043-0.0772-0.2086-0.0153-0.02630.0282-0.0787-0.29070.30360.04910.3926-0.08280.0150.6023-0.00960.464740.80087.9137-23.3954
50.61670.848-1.60691.9532-1.49395.24820.0982-0.00650.03670.43370.0546-0.0094-0.3204-0.1214-0.15280.43950.0296-0.01740.6708-0.00910.302721.34985.818717.1759
61.81190.02092.13170.2729-0.47213.8307-0.06060.3348-0.15250.21110.17330.085-0.78230.267-0.11270.5677-0.0590.15690.3764-0.02960.537542.1903-48.9381-11.7609
70.8769-0.12910.45172.665-0.71571.684-0.0683-0.03380.0226-0.07710.26070.18510.09690.4559-0.19250.22040.02210.08470.44830.0470.586634.2192-61.805-37.0254
80.4059-0.35160.20363.0535-0.56410.24570.0864-0.0852-0.3303-0.97960.13170.8093-0.0346-0.0564-0.21820.81280.0503-0.29380.20630.0160.603915.4912-37.7884-56.3798
90.6541.05690.00421.8447-0.09752.66230.0074-0.12430.3330.1194-0.10370.89710.2476-0.18470.09630.10670.10510.27420.31680.17351.1757.4669-59.0286-29.1241
101.24850.38792.74091.41770.78026.03840.0958-0.15280.01130.3521-0.03370.14670.1406-0.4291-0.06220.42250.04820.43230.73990.24910.5322.034-58.733513.9298
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 120
2X-RAY DIFFRACTION2A123 - 261
3X-RAY DIFFRACTION3A263 - 310
4X-RAY DIFFRACTION3A560 - 785
5X-RAY DIFFRACTION3A901
6X-RAY DIFFRACTION4A313 - 393
7X-RAY DIFFRACTION4A532 - 558
8X-RAY DIFFRACTION5A395 - 531
9X-RAY DIFFRACTION6B4 - 120
10X-RAY DIFFRACTION7B123 - 261
11X-RAY DIFFRACTION8B263 - 310
12X-RAY DIFFRACTION8B560 - 785
13X-RAY DIFFRACTION8B901
14X-RAY DIFFRACTION9B313 - 393
15X-RAY DIFFRACTION9B532 - 558
16X-RAY DIFFRACTION10B395 - 531

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