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- PDB-6lzi: Aquifex aeolicus MutL ATPase domain complexed with ADP -

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Basic information

Entry
Database: PDB / ID: 6lzi
TitleAquifex aeolicus MutL ATPase domain complexed with ADP
ComponentsDNA mismatch repair protein MutL
KeywordsDNA BINDING PROTEIN / DNA repair / ATPase
Function / homology
Function and homology information


mismatch repair complex / mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / ATP binding
Similarity search - Function
DNA mismatch repair protein, MutL / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain ...DNA mismatch repair protein, MutL / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / DNA mismatch repair protein, C-terminal domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / DNA mismatch repair protein MutL
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69105685009 Å
AuthorsFukui, K. / Izuhara, K. / Yano, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K07376 Japan
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A Lynch syndrome-associated mutation at a Bergerat ATP-binding fold destabilizes the structure of the DNA mismatch repair endonuclease MutL.
Authors: Izuhara, K. / Fukui, K. / Murakawa, T. / Baba, S. / Kumasaka, T. / Uchiyama, K. / Yano, T.
History
DepositionFeb 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 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

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Assembly

Deposited unit
A: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6468
Polymers35,6631
Non-polymers9827
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Gel filtration, DLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.017, 42.906, 53.845
Angle α, β, γ (deg.)80.978, 71.521, 77.707
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein DNA mismatch repair protein MutL


Mass: 35663.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 1-12, 43-44, 67-90, 216-217, 230-231, 258-260, 272-292, and 308-310 are disordered.
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: mutL, aq_1578 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: O67518
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 mM tris-HCl, 50 mM NaCl, 5 mM MgCl2, 5 mM ADP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 29323 / % possible obs: 92 % / Redundancy: 11.2 % / Biso Wilson estimate: 26.9081865961 Å2 / CC1/2: 0.78 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.041 / Net I/σ(I): 24.3
Reflection shellResolution: 1.69→1.73 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 2936 / Rpim(I) all: 0.43 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIXv1.10.1refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXv1.10.1phasing
Cootv0.7.2model building
PHENIXv1.10.1model building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5x9y

5x9y


Resolution: 1.69105685009→41.7270024284 Å / SU ML: 0.189017138443 / Cross valid method: FREE R-VALUE / σ(F): 263.488974409 / Phase error: 24.1340876785
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.242574382921 1824 6.81563410806 %
Rwork0.202383292 24938 -
obs0.205044957344 26762 82.8365369734 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.2810646356 Å2
Refinement stepCycle: LAST / Resolution: 1.69105685009→41.7270024284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 63 162 2186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01595770135962043
X-RAY DIFFRACTIONf_angle_d1.733262042682725
X-RAY DIFFRACTIONf_chiral_restr0.125374078001312
X-RAY DIFFRACTIONf_plane_restr0.00954226411044335
X-RAY DIFFRACTIONf_dihedral_angle_d22.0762710531270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6911-1.73680.2523360220781030.1752177426711411X-RAY DIFFRACTION61.1470113086
1.7368-1.78790.1876624093021280.1614793758131753X-RAY DIFFRACTION75.7551349174
1.7879-1.84560.2325681894181290.175395837491834X-RAY DIFFRACTION77.9896702424
1.8456-1.91160.2749105757311310.1847059023891726X-RAY DIFFRACTION76.4197530864
1.9116-1.98810.2339108682921490.1779438558351949X-RAY DIFFRACTION83.485873458
1.9881-2.07860.2171231936431510.172619751982063X-RAY DIFFRACTION88.9156626506
2.0786-2.18820.2358343870391550.1844861221842103X-RAY DIFFRACTION90.9017713366
2.1882-2.32520.2363884429191140.2028722845821586X-RAY DIFFRACTION68.4104627767
2.3252-2.50470.247176536441540.2148182779132119X-RAY DIFFRACTION91.6901976603
2.5047-2.75680.2727469510441540.2195443085872132X-RAY DIFFRACTION92.0660491341
2.7568-3.15560.2622411035541600.2232025176232183X-RAY DIFFRACTION94.0586109996
3.1556-3.97520.2326673403151430.2011089533611978X-RAY DIFFRACTION85.4208618607
3.9752-4.610.2381659636541530.2036554420742101X-RAY DIFFRACTION90.5948553055

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