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- PDB-9prp: N-terminal domain of E. coli MutL bound to NP660 -

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Basic information

Entry
Database: PDB / ID: 9prp
TitleN-terminal domain of E. coli MutL bound to NP660
ComponentsDNA mismatch repair protein MutL
KeywordsDNA BINDING PROTEIN / DNA repair / GHKL ATPase / Mismatch repair protein / MutL
Function / homology
Function and homology information


single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / 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 / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / 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
: / DNA mismatch repair protein MutL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRodriguez Gonzalez, J. / Guarne, A. / Blagg, J.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Cancer Discov / Year: 2026
Title: Pharmacological inhibition of PMS2 induces MMR deficiency and response to immune checkpoint blockade.
Authors: Blagg, J. / Riou, P. / Hervieu, A. / Piumatti, E. / Rodriguez-Plata, M.T. / Battuello, P. / Peall, A. / Amodio, V. / Vitiello, P.P. / Nightingale, D.J.H. / Bago, R. / Tongue, P. / Slater, T. ...Authors: Blagg, J. / Riou, P. / Hervieu, A. / Piumatti, E. / Rodriguez-Plata, M.T. / Battuello, P. / Peall, A. / Amodio, V. / Vitiello, P.P. / Nightingale, D.J.H. / Bago, R. / Tongue, P. / Slater, T. / Parmar, K. / Patel, P. / Rodriguez Gonzalez, J. / Clark, D.E. / Langley, G.W. / Nichols, C. / Guarne, A. / Winship, P.C.M. / Baker, M. / Drysdale, M. / Germano, G. / Bardelli, A.
History
DepositionJul 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: 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
B: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9884
Polymers78,5992
Non-polymers3882
Water2,216123
1
A: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4942
Polymers39,3001
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4942
Polymers39,3001
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.126, 69.694, 74.718
Angle α, β, γ (deg.)90.000, 113.740, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein DNA mismatch repair protein MutL


Mass: 39299.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mutL, b4170, JW4128 / Production host: Escherichia coli (E. coli) / References: UniProt: P23367
#2: Chemical ChemComp-A1CKR / 5-(cyclopentyloxy)benzene-1,3-diol


Mass: 194.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 21% PEG3350, 200 mM ammonium tartrate, 100 mM Bis-Tris, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.0332 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→48.82 Å / Num. obs: 37503 / % possible obs: 97.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 39.54 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1022 / Rpim(I) all: 0.06058 / Rrim(I) all: 0.1189 / Net I/σ(I): 8.27
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.9 % / Num. unique obs: 2836 / CC1/2: 0.584 / % possible all: 97.01

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSv3-16-0data reduction
DIALSv3-16-0data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.82 Å / SU ML: 0.4113 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.8692
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2954 1860 5 %
Rwork0.2375 35368 -
obs0.2404 37228 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.74 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4809 0 28 123 4960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784913
X-RAY DIFFRACTIONf_angle_d0.88516662
X-RAY DIFFRACTIONf_chiral_restr0.051769
X-RAY DIFFRACTIONf_plane_restr0.0083874
X-RAY DIFFRACTIONf_dihedral_angle_d16.49481798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.42261410.41432685X-RAY DIFFRACTION97.01
2.16-2.220.43341380.38572684X-RAY DIFFRACTION96.98
2.22-2.290.39671420.36022673X-RAY DIFFRACTION96.57
2.29-2.370.35521410.32262666X-RAY DIFFRACTION97.09
2.37-2.470.32851430.30212728X-RAY DIFFRACTION97.26
2.47-2.580.34431430.28652702X-RAY DIFFRACTION97.6
2.58-2.720.36861430.27152699X-RAY DIFFRACTION97.76
2.72-2.890.33341440.2672720X-RAY DIFFRACTION97.68
2.89-3.110.30061450.25282723X-RAY DIFFRACTION98.46
3.11-3.420.29151450.23192754X-RAY DIFFRACTION98.44
3.42-3.920.30741420.20172760X-RAY DIFFRACTION98.61
3.92-4.940.22921460.18182769X-RAY DIFFRACTION98.51
4.94-48.820.24451470.19412805X-RAY DIFFRACTION98.11

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