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- PDB-8h1f: Aquifex aeolicus MutL endonuclease domain complexed with zinc ion... -

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Basic information

Entry
Database: PDB / ID: 8h1f
TitleAquifex aeolicus MutL endonuclease domain complexed with zinc ions after soaking
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 support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K07376 Japan
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)12,99811
Polymers12,3521
Non-polymers64610
Water2,198122
1
A: DNA mismatch repair protein MutL
hetero molecules

A: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,99622
Polymers24,7052
Non-polymers1,29120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4600 Å2
ΔGint-331 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.529, 35.529, 167.288
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) / Strain (production host): Rosetta2 / References: UniProt: O67518
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 200 mM sodium acetate (pH 4.6), 100 mM CdCl2, and 30 % (v/v) polyethylene glycol 300

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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: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.22→34.75 Å / Num. obs: 33167 / % possible obs: 99.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 12.99 Å2 / CC1/2: 0.91 / Rpim(I) all: 0.02 / Net I/σ(I): 57.2
Reflection shellResolution: 1.22→1.26 Å / Mean I/σ(I) obs: 4.2 / Num. unique obs: 3220 / CC1/2: 0.93 / Rpim(I) all: 0.17

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Processing

Software
NameVersionClassification
PRIME-X1.19.2-4158refinement
PHENIX1.19.2-4158model building
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
Coot0.7.2model building
RefinementMethod to determine structure: SAD / Resolution: 1.22→34.75 Å / SU ML: 0.1027 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.1003
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1754 2000 6.03 %
Rwork0.1572 31167 -
obs0.1583 33167 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.7 Å2
Refinement stepCycle: LAST / Resolution: 1.22→34.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms847 0 22 122 991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061878
X-RAY DIFFRACTIONf_angle_d0.86611179
X-RAY DIFFRACTIONf_chiral_restr0.072126
X-RAY DIFFRACTIONf_plane_restr0.0085148
X-RAY DIFFRACTIONf_dihedral_angle_d14.9823344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.250.25371370.192130X-RAY DIFFRACTION99.3
1.25-1.280.23251390.14822182X-RAY DIFFRACTION99.49
1.28-1.320.14391410.13182185X-RAY DIFFRACTION99.61
1.32-1.360.17681390.13342173X-RAY DIFFRACTION99.7
1.36-1.410.15951390.13772164X-RAY DIFFRACTION99.87
1.41-1.470.17311430.11982217X-RAY DIFFRACTION99.96
1.47-1.540.14731390.11532174X-RAY DIFFRACTION100
1.54-1.620.14431430.11682232X-RAY DIFFRACTION99.96
1.62-1.720.14061400.12782186X-RAY DIFFRACTION100
1.72-1.850.1561440.13992248X-RAY DIFFRACTION100
1.85-2.040.18411450.13972233X-RAY DIFFRACTION100
2.04-2.330.17791450.1512269X-RAY DIFFRACTION100
2.33-2.940.18371480.18262319X-RAY DIFFRACTION100
2.94-100.19591580.18382455X-RAY DIFFRACTION99.24

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