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- PDB-6lzj: Aquifex aeolicus MutL ATPase domain complexed with AMPPCP -

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Basic information

Entry
Database: PDB / ID: 6lzj
TitleAquifex aeolicus MutL ATPase domain complexed with AMPPCP
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / DNA mismatch repair protein MutL
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72835563454 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)36,1933
Polymers35,6631
Non-polymers5302
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Gel filtration, DLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-10 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.016, 42.863, 53.859
Angle α, β, γ (deg.)81.110, 71.598, 77.691
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, 68-90, 216-217, 231, 259, 273-292, and 306-310 are disordered.
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Strain: VF5 / Gene: mutL / Plasmid: pET-11a / 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-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 41.2 %
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 AMPPCP

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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: 1.728→33.85 Å / Num. obs: 27191 / % possible obs: 92.2 % / Redundancy: 7.8 % / Biso Wilson estimate: 28.2509524166 Å2 / CC1/2: 0.75 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.041 / Net I/σ(I): 25.5
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 2818 / Rpim(I) all: 0.458 / % possible all: 96.1

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Processing

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

5x9y


Resolution: 1.72835563454→33.8470218389 Å / SU ML: 0.166573750674 / Cross valid method: FREE R-VALUE / σ(F): 4.9219533031 / Phase error: 23.4865123955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234289477111 1997 7.35489098409 %
Rwork0.208637409745 25155 -
obs0.210518540207 27152 89.6875206448 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.9128505527 Å2
Refinement stepCycle: LAST / Resolution: 1.72835563454→33.8470218389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 32 139 2170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01035995521892056
X-RAY DIFFRACTIONf_angle_d1.298968892952756
X-RAY DIFFRACTIONf_chiral_restr0.0704865882669314
X-RAY DIFFRACTIONf_plane_restr0.0087219584007342
X-RAY DIFFRACTIONf_dihedral_angle_d21.27297799931272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7284-1.77160.196684003842990.1455532661891253X-RAY DIFFRACTION62.4192059095
1.7716-1.81950.1828302375881530.1486582851021920X-RAY DIFFRACTION95.6180811808
1.8195-1.8730.2265026711091520.1850118670511910X-RAY DIFFRACTION95.6400742115
1.873-1.93350.2887494197971180.2600622570441509X-RAY DIFFRACTION74.6672785682
1.9335-2.00260.2642749421831530.2052164335731913X-RAY DIFFRACTION96.2721342032
2.0026-2.08270.2366220732361520.1931263983241931X-RAY DIFFRACTION96.0793357934
2.0827-2.17750.2245913900961550.2058053363591940X-RAY DIFFRACTION96.5437788018
2.1775-2.29230.2964495037811100.2643904926151381X-RAY DIFFRACTION69.6403549743
2.2923-2.43590.2451340112061570.2193775924521972X-RAY DIFFRACTION97.4816849817
2.4359-2.62390.2588919079791540.2273804387361946X-RAY DIFFRACTION97.7198697068
2.6239-2.88780.2668549398061560.2208522280321970X-RAY DIFFRACTION98.1532779317
2.8878-3.30530.2574330541121560.2187072787191958X-RAY DIFFRACTION98.417132216
3.3053-4.16320.1935445086141270.1922065141411597X-RAY DIFFRACTION79.593721145
4.1632-4.750.2207771476071550.1953445798811955X-RAY DIFFRACTION97.5046210721
Refinement TLS params.Method: refined / Origin x: 14.9546732781 Å / Origin y: 29.613288474 Å / Origin z: -26.1773897294 Å
111213212223313233
T0.163315155728 Å20.0180756774053 Å20.00619754492888 Å2-0.180227536401 Å2-0.0143517486578 Å2--0.164376002564 Å2
L0.484412530205 °20.6607421299 °2-0.0572045594144 °2-1.89171944658 °2-0.176479303207 °2--0.651943227941 °2
S0.0538800782265 Å °-0.0301316462491 Å °-0.00494451457011 Å °0.247508386031 Å °-0.0282310301645 Å °-0.139642096119 Å °-0.0131987153181 Å °-0.0488250258892 Å °-0.000181294894779 Å °
Refinement TLS groupSelection details: (chain A and resseq 12:303)

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