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- PDB-8h1e: Aquifex aeolicus MutL endonuclease domain complexed with manganes... -

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Basic information

Entry
Database: PDB / ID: 8h1e
TitleAquifex aeolicus MutL endonuclease domain complexed with manganese ions
ComponentsDNA mismatch repair protein MutL
KeywordsDNA BINDING PROTEIN / endonuclease
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
: / DI(HYDROXYETHYL)ETHER / DNA mismatch repair protein MutL
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.22 Å
AuthorsFukui, K. / Yano, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Life Sci Alliance / Year: 2023
Title: Catalytic mechanism of the zinc-dependent MutL endonuclease reaction.
Authors: Fukui, K. / Yamamoto, T. / Murakawa, T. / Baba, S. / Kumasaka, T. / Yano, T.
History
DepositionOct 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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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)12,7888
Polymers12,3521
Non-polymers4367
Water1,26170
1
A: DNA mismatch repair protein MutL
hetero molecules

A: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,57616
Polymers24,7052
Non-polymers87114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4370 Å2
ΔGint-62 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.631, 35.631, 167.819
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein DNA mismatch repair protein MutL


Mass: 12352.259 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Strain: VF5 / Gene: mutL / Production host: Escherichia coli (E. coli) / References: UniProt: O67518
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 200 mM sodium acetate, 50 mM MnCl2, and 30 % (v/v) polyethylene glycol 400

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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: Jun 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.22→32.8 Å / Num. obs: 33594 / % possible obs: 99.7 % / Redundancy: 14.4 % / Biso Wilson estimate: 17.91 Å2 / CC1/2: 0.95 / Net I/σ(I): 60
Reflection shellResolution: 1.22→1.26 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3304 / CC1/2: 0.59 / Rpim(I) all: 0.53

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
PHENIX1.19.2-4158-000model building
Coot0.7.2model building
RefinementMethod to determine structure: SAD
Starting model: 5B42

5b42


Resolution: 1.22→32.8 Å / SU ML: 0.149 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.8343
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2212 1996 5.94 %
Rwork0.1997 31598 -
obs0.2011 33594 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.47 Å2
Refinement stepCycle: LAST / Resolution: 1.22→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms860 0 13 70 943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062892
X-RAY DIFFRACTIONf_angle_d0.89411201
X-RAY DIFFRACTIONf_chiral_restr0.082127
X-RAY DIFFRACTIONf_plane_restr0.009153
X-RAY DIFFRACTIONf_dihedral_angle_d16.7462355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.250.36771390.36292195X-RAY DIFFRACTION99.62
1.25-1.280.30821410.31142219X-RAY DIFFRACTION99.79
1.28-1.320.26541390.2672220X-RAY DIFFRACTION100
1.32-1.360.25251400.22272210X-RAY DIFFRACTION100
1.36-1.410.2441390.21342205X-RAY DIFFRACTION99.91
1.41-1.470.21171410.20262215X-RAY DIFFRACTION99.92
1.47-1.530.24081410.19912238X-RAY DIFFRACTION99.71
1.53-1.620.20091430.1762241X-RAY DIFFRACTION99.83
1.62-1.720.22991400.18032234X-RAY DIFFRACTION99.58
1.72-1.850.2091410.17182239X-RAY DIFFRACTION99.33
1.85-2.030.24181410.182249X-RAY DIFFRACTION99.09
2.03-2.330.20551460.18842305X-RAY DIFFRACTION99.8
2.33-2.930.25011480.21242343X-RAY DIFFRACTION99.84
2.93-32.80.2011570.19842485X-RAY DIFFRACTION98.77

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