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- PDB-7rcb: Crystal Structure of a PMS2 VUS -

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Basic information

Entry
Database: PDB / ID: 7rcb
TitleCrystal Structure of a PMS2 VUS
ComponentsMismatch repair endonuclease PMS2
KeywordsHYDROLASE / Mismatch Repair / Variant of Uncertain Significance / ATPase Domain / DNA Repair Enzyme
Function / homology
Function and homology information


single base insertion or deletion binding / Defective Mismatch Repair Associated With MLH1 / Defective Mismatch Repair Associated With PMS2 / MutLalpha complex / somatic recombination of immunoglobulin gene segments / positive regulation of isotype switching to IgA isotypes / positive regulation of isotype switching to IgG isotypes / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / ATP-dependent DNA damage sensor activity ...single base insertion or deletion binding / Defective Mismatch Repair Associated With MLH1 / Defective Mismatch Repair Associated With PMS2 / MutLalpha complex / somatic recombination of immunoglobulin gene segments / positive regulation of isotype switching to IgA isotypes / positive regulation of isotype switching to IgG isotypes / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / ATP-dependent DNA damage sensor activity / somatic hypermutation of immunoglobulin genes / mismatch repair / TP53 Regulates Transcription of DNA Repair Genes / endonuclease activity / Hydrolases; Acting on ester bonds / response to xenobiotic stimulus / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
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 ...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
Mismatch repair endonuclease PMS2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsD'Arcy, B.M. / Prakash, A.
CitationJournal: Mol Genet Genomic Med / Year: 2022
Title: PMS2 variant results in loss of ATPase activity without compromising mismatch repair.
Authors: D'Arcy, B.M. / Arrington, J. / Weisman, J. / McClellan, S.B. / Yang, Z. / Deivanayagam, C. / Blount, J. / Prakash, A.
History
DepositionJul 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mismatch repair endonuclease PMS2
B: Mismatch repair endonuclease PMS2


Theoretical massNumber of molelcules
Total (without water)80,9722
Polymers80,9722
Non-polymers00
Water7,224401
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.219, 75.262, 134.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 33 through 44 or resid 46...
d_2ens_1(chain "B" and (resid 33 through 44 or resid 46...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUGLUA2 - 13
d_12ens_1SERTHRA15 - 53
d_13ens_1ALAASPA58 - 281
d_14ens_1GLUASPA286 - 303
d_21ens_1LEUGLUB1 - 12
d_22ens_1SERTHRB14 - 52
d_23ens_1ALAASPB54 - 295

NCS oper: (Code: givenMatrix: (-0.00682959365487, 0.99986708062, -0.0148046527549), (0.999447839435, 0.00634380433234, -0.0326155238337), (-0.0325172707782, -0.0150192289841, -0.999358319054)Vector: - ...NCS oper: (Code: given
Matrix: (-0.00682959365487, 0.99986708062, -0.0148046527549), (0.999447839435, 0.00634380433234, -0.0326155238337), (-0.0325172707782, -0.0150192289841, -0.999358319054)
Vector: -16.1617809975, 17.6195503895, -100.853549334)

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Components

#1: Protein Mismatch repair endonuclease PMS2 / DNA mismatch repair protein PMS2 / PMS1 protein homolog 2


Mass: 40486.207 Da / Num. of mol.: 2 / Mutation: N335S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PMS2, PMSL2 / Plasmid: pET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 (DE3 pLysS)
References: UniProt: P54278, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 1:1 7.5 mg/mL protein with 8% v/v Tacsimate, pH 5.8, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→34.34 Å / Num. obs: 51950 / % possible obs: 98.83 % / Redundancy: 7.9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07765 / Rpim(I) all: 0.02862 / Rrim(I) all: 0.083 / Χ2: 1 / Net I/σ(I): 19.71
Reflection shellResolution: 2→2.071 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.8954 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5160 / CC1/2: 0.739 / CC star: 0.922 / Rpim(I) all: 0.3435 / Rrim(I) all: 0.9616 / Χ2: 1 / % possible all: 99.46

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Processing

Software
NameVersionClassification
SAINTdata reduction
SADABSdata scaling
PHASERphasing
PHENIXV1.19refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1H7S

1h7s


Resolution: 2→34.34 Å / Cross valid method: FREE R-VALUE / σ(F): 15.57 / Phase error: 24.2702
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1979 5321 10.24 %
Rwork0.1617 46629 -
obs0.167 51950 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.37 Å2
Refinement stepCycle: LAST / Resolution: 2→34.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4487 0 0 401 4888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034571
X-RAY DIFFRACTIONf_angle_d0.57796202
X-RAY DIFFRACTIONf_chiral_restr0.0438736
X-RAY DIFFRACTIONf_plane_restr0.0047801
X-RAY DIFFRACTIONf_dihedral_angle_d12.52051635
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.825705043177 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.32862450.26942232X-RAY DIFFRACTION85.95
2.03-2.070.29412570.25942305X-RAY DIFFRACTION89.65
2.07-2.110.28812880.23932282X-RAY DIFFRACTION88.42
2.11-2.150.23232760.23072370X-RAY DIFFRACTION89.5
2.15-2.20.24472690.21472295X-RAY DIFFRACTION89.33
2.2-2.250.21842870.20572303X-RAY DIFFRACTION88.65
2.25-2.310.21382330.20212362X-RAY DIFFRACTION90.85
2.31-2.370.23212370.19932392X-RAY DIFFRACTION90.71
2.37-2.440.23242820.18662292X-RAY DIFFRACTION88.8
2.44-2.520.23312520.1842356X-RAY DIFFRACTION89.96
2.52-2.610.19392620.17162353X-RAY DIFFRACTION89.64
2.61-2.710.24272750.16982321X-RAY DIFFRACTION88.96
2.71-2.830.20542640.17372334X-RAY DIFFRACTION89.36
2.83-2.980.18952670.1632355X-RAY DIFFRACTION89.2
2.98-3.170.19712320.15662378X-RAY DIFFRACTION89.87
3.17-3.410.17222250.14512382X-RAY DIFFRACTION89.95
3.42-3.760.19352820.13792327X-RAY DIFFRACTION87.51
3.76-4.30.15762940.12662323X-RAY DIFFRACTION87.07
4.3-5.420.15112880.12012325X-RAY DIFFRACTION85.76
5.42-34.340.2022520.16082396X-RAY DIFFRACTION84.57
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)
11.56395605117-0.5709828386660.02966690572461.92052651333-0.4067108285621.07662227917-0.0460890843316-0.0941692511304-0.09676456457790.0892561684051-0.0164831021914-0.08223978190290.01373844509570.1156112196620.06036445314350.202707708917-0.00670284525865-0.008407227500770.1291281216513.66301397892E-50.1246481019584.763686938375.44969592043-38.3090555527
21.57708494367-0.765804967035-0.9382455866013.002743667641.826176273822.18133603619-0.0148112414719-0.143418044249-0.02825693443360.441673215459-0.1443032642230.3736718009270.30598921822-0.2187595821970.1077708527420.248653493438-0.03789653411140.04071734439910.1828727571570.0007141523008840.218860121273-18.550815236119.8223835085-28.4890067983
34.950875821620.08757697181980.278885227121.7604101342-0.03548662569241.26927309039-0.08426955620860.04866115430790.313067073951-0.003819879073380.124414696817-0.146900003326-0.02842460167060.105806209728-0.001611343207210.237245669386-0.00854288240844-0.01640431898820.231817722621-0.01069564781850.167894252742-6.5857564624420.1452996278-61.576038217
44.310627199740.6320168840232.248709675161.333651745371.262542523131.87424347552-0.1087308965370.5678146066390.634257101225-0.2553814722120.168898081522-0.33389867471-0.536554923570.3967062358940.05507984694390.346923511788-0.0877756501458-0.01702527964260.3826755568070.06767770519180.365175584562-8.3110144253933.2618266099-67.3325853236
53.04947977927-1.071769304360.1384257285251.50364380685-0.3177527466061.09920553947-0.131893896063-0.01737977590520.2691467178940.01620426048860.134871066318-0.0112378773622-0.1688978472270.03786126196990.002885257903760.220089632604-0.00710532707418-0.01601496262160.203819822529-0.002068171474160.110617042832-12.183823940123.5704859933-62.0924850376
62.47734816007-0.605241516996-1.199516463471.546341526320.669341227211.81638963915-0.244032825380.280314200722-0.335856994633-0.2061505150490.0934865427932-0.09460342478240.1936202950340.0226113618910.154064147460.261242046946-0.05268123516360.04737896840170.216930107739-0.03298943822140.1812334733984.588541506962.30639569681-67.1029890082
71.83840327204-0.28095352462-0.9509366924651.649155071511.214943764481.47979229975-0.3449256165440.617673553088-0.52712990789-0.3634299453130.05081349645260.1738313397920.50034030115-0.556557311870.3587421076430.458859588211-0.1586798948690.04779233601350.478067851714-0.1343860517690.327850069088-0.68190588309-4.37763131258-73.8909546147
83.72315043276-0.317742283824-1.259536271990.9791727555311.592890046392.78171945802-0.3136367164360.722825016122-0.388010112622-0.579212496993-0.0493366126973-0.1897699294230.206815973192-0.3975514759740.1097020080130.419518938469-0.07526049144570.08778634468810.397369017819-0.08954341888970.2489651912249.814016084970.404078434862-79.1067529146
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 32 through 194 )AA32 - 1941 - 142
22chain 'A' and (resid 195 through 365 )AA195 - 365143 - 304
33chain 'B' and (resid 33 through 76 )BB33 - 761 - 44
44chain 'B' and (resid 77 through 117 )BB77 - 11745 - 61
55chain 'B' and (resid 118 through 194 )BB118 - 19462 - 138
66chain 'B' and (resid 195 through 274 )BB195 - 274139 - 218
77chain 'B' and (resid 275 through 320 )BB275 - 320219 - 264
88chain 'B' and (resid 321 through 364 )BB321 - 364265 - 295

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