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- PDB-4p7a: Crystal Structure of human MLH1 -

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Basic information

Entry
Database: PDB / ID: 4p7a
TitleCrystal Structure of human MLH1
ComponentsDNA mismatch repair protein Mlh1
KeywordsDNA BINDING PROTEIN / structural genomics consortium / DNA MISMATCH REPAIR / DNA DAMAGE / SGC
Function / homology
Function and homology information


chiasma / late recombination nodule / male meiosis chromosome segregation / meiotic metaphase I homologous chromosome alignment / Defective Mismatch Repair Associated With MLH1 / Defective Mismatch Repair Associated With PMS2 / negative regulation of mitotic recombination / meiotic spindle midzone assembly / MutLalpha complex / guanine/thymine mispair binding ...chiasma / late recombination nodule / male meiosis chromosome segregation / meiotic metaphase I homologous chromosome alignment / Defective Mismatch Repair Associated With MLH1 / Defective Mismatch Repair Associated With PMS2 / negative regulation of mitotic recombination / meiotic spindle midzone assembly / MutLalpha complex / guanine/thymine mispair binding / meiotic telomere clustering / positive regulation of isotype switching to IgA isotypes / nuclear-transcribed mRNA poly(A) tail shortening / resolution of meiotic recombination intermediates / homologous chromosome pairing at meiosis / positive regulation of isotype switching to IgG isotypes / synaptonemal complex / female meiosis chromosome segregation / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / isotype switching / ATP-dependent DNA damage sensor activity / oogenesis / somatic hypermutation of immunoglobulin genes / mismatch repair / male germ cell nucleus / TP53 Regulates Transcription of DNA Repair Genes / response to bacterium / Meiotic recombination / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / chromosome / spermatogenesis / chromatin binding / enzyme binding / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / nucleus
Similarity search - Function
DNA mismatch repair protein Mlh1, C-terminal / DNA mismatch repair protein Mlh1 C-terminus / 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 / Ribosomal Protein S5; domain 2 - #10 ...DNA mismatch repair protein Mlh1, C-terminal / DNA mismatch repair protein Mlh1 C-terminus / 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 / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA mismatch repair protein Mlh1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsTempel, W. / Lam, R. / Zeng, H. / Walker, J.R. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome.
Authors: Wu, H. / Zeng, H. / Lam, R. / Tempel, W. / Kerr, I.D. / Min, J.
History
DepositionMar 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
SupersessionNov 12, 2014ID: 3NA3
Revision 1.1Nov 12, 2014Group: Other
Revision 1.2Dec 16, 2015Group: Database references
Revision 2.0Jul 17, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / pdbx_struct_oper_list ...atom_site / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / software / struct_keywords
Item: _atom_site.pdbx_PDB_model_num / _pdbx_struct_oper_list.symmetry_operation ..._atom_site.pdbx_PDB_model_num / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.PDB_model_num / _pdbx_unobs_or_zero_occ_residues.PDB_model_num / _pdbx_validate_torsion.PDB_model_num / _software.classification / _software.name / _software.version / _struct_keywords.pdbx_keywords
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA mismatch repair protein Mlh1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,10712
Polymers38,6551
Non-polymers45211
Water63135
1
A: DNA mismatch repair protein Mlh1
hetero molecules

A: DNA mismatch repair protein Mlh1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,21324
Polymers77,3102
Non-polymers90322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area4850 Å2
ΔGint-51 kcal/mol
Surface area27860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.568, 94.568, 85.825
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Detailshas not been determined as part of this study.

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Components

#1: Protein DNA mismatch repair protein Mlh1 / MutL protein homolog 1


Mass: 38655.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLH1, COCA2 / Plasmid: PET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-PRARE2 / References: UniProt: P40692
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 9 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG4000, 10% ISOPROPANOL, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→47.28 Å / Num. obs: 19468 / % possible obs: 99.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.02 / Net I/σ(I): 27.1 / Num. measured all: 184048
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.113 / Mean I/σ(I) obs: 2.3 / Num. measured all: 17980 / Num. unique all: 1888 / Rpim(I) all: 0.382 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
Aimless0.1.29data scaling
BUSTERrefinement
XDSdata reduction
PDB_EXTRACT3.14data extraction
RefinementResolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.2403 / WRfactor Rwork: 0.1939 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8213 / SU B: 11.41 / SU ML: 0.153 / SU R Cruickshank DPI: 0.236 / SU Rfree: 0.2095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: This entry is a re-interpretation of the data underlying entry 3NA3. Autobuster was used during intermediate refinement steps. COOT was used for interactive model building. Model geometry ...Details: This entry is a re-interpretation of the data underlying entry 3NA3. Autobuster was used during intermediate refinement steps. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 981 5 %RANDOM
Rwork0.2026 18456 --
obs0.2051 19437 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 153.24 Å2 / Biso mean: 65.1682 Å2 / Biso min: 28.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å2-0 Å2
3----2.4 Å2
Refinement stepCycle: final / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2195 0 37 37 2269
Biso mean--39.86 43.95 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192284
X-RAY DIFFRACTIONr_bond_other_d0.0020.022127
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9743114
X-RAY DIFFRACTIONr_angle_other_deg0.834852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5345305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59123.8184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30715348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8981514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022621
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02500
X-RAY DIFFRACTIONr_mcbond_it2.9913.6021223
X-RAY DIFFRACTIONr_mcbond_other2.9833.61222
X-RAY DIFFRACTIONr_mcangle_it4.1415.3841527
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 70 -
Rwork0.282 1367 -
all-1437 -
obs--99.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0232-0.3371.20986.3497-1.55151.02130.0221-0.0804-0.0357-0.1388-0.0573-0.34750.0244-0.00340.03530.1838-0.031-0.03930.1722-0.01530.199435.137-56.678818.5016
23.9262-0.0340.34044.3785-1.18653.28740.1170.0189-0.19670.0611-0.2644-0.24920.09960.23470.14740.0519-0.00030.02130.02620.00820.129826.7544-20.4778.983
33.3020.2110.86135.74931.75036.9218-0.15830.6624-0.464-0.2720.09460.01540.735-0.13020.06370.3324-0.0211-0.13690.4644-0.09240.394714.8412-22.4485-17.1678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 11
2X-RAY DIFFRACTION2A12 - 209
3X-RAY DIFFRACTION3A210 - 336

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