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- PDB-8xla: Mismatch Repair Complex -

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Basic information

Entry
Database: PDB / ID: 8xla
TitleMismatch Repair Complex
Components
  • Beta sliding clamp
  • DNA mismatch repair protein MutL
KeywordsDNA BINDING PROTEIN / DNA Mismatch Repair / Endonuclease / processivity clamp
Function / homology
Function and homology information


mismatch repair complex / mismatched DNA binding / DNA polymerase III complex / ATP-dependent DNA damage sensor activity / DNA strand elongation involved in DNA replication / mismatch repair / 3'-5' exonuclease activity / DNA-directed DNA polymerase activity / ATP hydrolysis activity / DNA binding ...mismatch repair complex / mismatched DNA binding / DNA polymerase III complex / ATP-dependent DNA damage sensor activity / DNA strand elongation involved in DNA replication / mismatch repair / 3'-5' exonuclease activity / DNA-directed DNA polymerase activity / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm
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 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / : / 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 / Beta sliding clamp
Similarity search - Component
Biological speciesNeisseria gonorrhoeae FA 1090 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsNirwal, S. / Nair, D.T.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT.MED-II/ATPC/BSC/01/2010 India
Citation
Journal: Nucleic Acids Res. / Year: 2025
Title: The structure of the MutL-CTD:processivity-clamp complex provides insight regarding strand discrimination in non-methyl-directed DNA mismatch repair.
Authors: Nirwal, S. / Jha, R. / Narayanan, N. / Sharma, M. / Kulkarni, D.S. / Sharma, D. / Babu, A.S. / Suthar, D.K. / Rao, D.N. / Nair, D.T.
#1: Journal: Nucleic Acids Res / Year: 2025
Title: The structure of the MutL-CTD:processivity-clamp complex provides insight regarding strand discrimination in non-methyl-directed DNA mismatch repair.
Authors: Nirwal, S. / Jha, R. / Narayanan, N. / Sharma, M. / Kulkarni, D.S. / Sharma, D. / Babu, A.S. / Suthar, D.K. / Rao, D.N. / Nair, D.T.
History
DepositionDec 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta sliding clamp
B: Beta sliding clamp
E: Beta sliding clamp
F: Beta sliding clamp
Y: DNA mismatch repair protein MutL
Z: DNA mismatch repair protein MutL
D: DNA mismatch repair protein MutL


Theoretical massNumber of molelcules
Total (without water)244,2547
Polymers244,2547
Non-polymers00
Water00
1
A: Beta sliding clamp
B: Beta sliding clamp
E: Beta sliding clamp
F: Beta sliding clamp
Y: DNA mismatch repair protein MutL
Z: DNA mismatch repair protein MutL
D: DNA mismatch repair protein MutL

A: Beta sliding clamp
B: Beta sliding clamp
E: Beta sliding clamp
F: Beta sliding clamp
Y: DNA mismatch repair protein MutL
Z: DNA mismatch repair protein MutL
D: DNA mismatch repair protein MutL


Theoretical massNumber of molelcules
Total (without water)488,50814
Polymers488,50814
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_857-x+3,y,-z+21
Buried area32350 Å2
ΔGint-167 kcal/mol
Surface area180610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.750, 212.040, 255.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
Beta sliding clamp / Processivity Clamp


Mass: 43081.332 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae FA 1090 (bacteria)
Gene: NGO_0002 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q5FAJ1
#2: Protein DNA mismatch repair protein MutL


Mass: 23976.260 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae FA 1090 (bacteria)
Gene: mutL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q5F8M6
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: 4.63 Å3/Da / Density % sol: 73 % / Description: Half moon shaped crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 10-14% (w/v) PEG 5000 MME, 0.1M citrate buffer (pH 5.5), 0.2-0.5M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97864 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97864 Å / Relative weight: 1
ReflectionResolution: 3.5→68.13 Å / Num. obs: 54175 / % possible obs: 98.3 % / Redundancy: 5.4 % / Biso Wilson estimate: 112.84 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.06 / Net I/σ(I): 18
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4442 / CC1/2: 0.598 / Rpim(I) all: 0.524 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLM7.3.0data reduction
Aimless7.1.012data scaling
PHASER7.1.012phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→64.7 Å / SU ML: 0.5137 / Cross valid method: FREE R-VALUE / σ(F): 0.37 / Phase error: 30.7278
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2798 5166 5.08 %RANDOM
Rwork0.2669 96619 --
obs0.2675 54043 95.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 122.87 Å2
Refinement stepCycle: LAST / Resolution: 3.5→64.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15581 0 0 0 15581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005215816
X-RAY DIFFRACTIONf_angle_d0.775921407
X-RAY DIFFRACTIONf_chiral_restr0.04622495
X-RAY DIFFRACTIONf_plane_restr0.00432815
X-RAY DIFFRACTIONf_dihedral_angle_d14.54795920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.540.37921910.37473176X-RAY DIFFRACTION95.06
3.54-3.580.36641800.38263188X-RAY DIFFRACTION95.46
3.58-3.630.39212090.35493194X-RAY DIFFRACTION95.27
3.63-3.670.41731610.34883211X-RAY DIFFRACTION95.15
3.67-3.720.29122030.35453157X-RAY DIFFRACTION95.32
3.72-3.770.33771390.33023270X-RAY DIFFRACTION95.41
3.77-3.820.34211750.31833232X-RAY DIFFRACTION95.65
3.82-3.880.29671700.31463211X-RAY DIFFRACTION95.81
3.88-3.940.35612020.31433202X-RAY DIFFRACTION95.7
3.94-4.010.32151810.31053242X-RAY DIFFRACTION95.99
4.01-4.080.35351470.31183212X-RAY DIFFRACTION95.59
4.08-4.150.3261390.30723258X-RAY DIFFRACTION95.77
4.15-4.230.33011650.31973266X-RAY DIFFRACTION95.89
4.23-4.320.27761480.2743242X-RAY DIFFRACTION95.84
4.32-4.410.31151820.26193215X-RAY DIFFRACTION95.91
4.41-4.510.2181510.23213317X-RAY DIFFRACTION96.36
4.51-4.620.22791880.23223175X-RAY DIFFRACTION96.06
4.62-4.750.21211610.21893237X-RAY DIFFRACTION95.93
4.75-4.890.24241960.23053237X-RAY DIFFRACTION96.03
4.89-5.050.27691720.24083223X-RAY DIFFRACTION96.12
5.05-5.230.30461700.26373213X-RAY DIFFRACTION95.65
5.23-5.440.34111710.26493261X-RAY DIFFRACTION95.81
5.44-5.680.30571350.28533223X-RAY DIFFRACTION95.72
5.68-5.980.30331690.28913258X-RAY DIFFRACTION95.81
5.98-6.360.36741720.29353236X-RAY DIFFRACTION95.89
6.36-6.850.28271940.28423184X-RAY DIFFRACTION95.61
6.85-7.540.28061460.2583237X-RAY DIFFRACTION95.59
7.54-8.620.24062000.23283200X-RAY DIFFRACTION95.69
8.63-10.860.19041720.20213214X-RAY DIFFRACTION94.98
10.86-64.70.22971770.23413128X-RAY DIFFRACTION93.12
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)
12.517668892141.913422526920.8354126179783.222619492981.153530045390.9237733394950.0109562895666-0.160283365618-0.1918302417150.0873108775912-0.1050402186120.4712560241730.395194029455-0.1552496899260.09942142906870.8952894679070.04061219476240.127047884830.5580891097390.1016798540991.08645829765202.928718849229.942844991315.23123668
22.062639714781.436136322460.694435853242.251767789980.6711218116621.51349618479-0.4473621819720.997220888529-0.130887066063-0.6010302272410.45511387731-0.02670448774420.125102241450.4298792912570.0008970292396460.95280022963-0.0226168748580.009505593178641.300684355450.03393882412850.571873085194220.262790484241.480031578280.850044413
35.171270277161.47577666836-0.9424546849080.843242945986-0.9213843893672.34932397604-0.3411788877581.073851981960.449415025771-0.8626054033590.2855340952180.0677519893432-0.0175898364709-0.4292891355080.355320237812.234044063390.183556138313-0.1421379602171.457894369380.1680260917091.20553545542216.059613601266.761507199253.387894002
44.475577300461.697691947620.9788226454092.06533249538-0.4007591435241.14997955286-0.2859826900951.416359178630.565097833842-0.3536040917040.322846886259-0.114939803538-0.28019175481-0.0400271997208-0.05230289803791.10796989420.1898906309050.256564868431.26198605110.1628324433520.835911701878185.41111031289.420285104303.96911374
55.932287894780.9180230694370.1281817597991.95199642621-0.3026822003351.210942750130.0108607405052-0.6951681330550.02955271555020.3210731752560.0001813026307-0.162733230423-0.173677072519-0.05157471835860.01128571727310.8637951228240.1751438273040.0022866660870.590986511952-0.05380976754280.634052883299201.45317054272.402283212337.142748664
62.159493838911.2920131012-0.2580932674443.82137668091-0.4008877907591.714425490850.4729481898640.07823795156550.2716194744860.140610887886-0.5384826844150.8121210098-0.438617363986-0.350269426940.238487718311.364454911960.2453365920090.08367299563851.39397213119-0.01012949968721.35258514425202.615108973271.614710218279.423586221
7-0.0563229342106-0.3182457044370.5867275402272.59150582778-2.472200693932.107883249960.09484709098310.1056495379320.140491674486-0.2571592840010.3855871548940.6241926868640.172002908529-0.506882329591-0.4603162103251.62238554511-0.03820589138350.08633762247371.452381272480.02076871719861.93422155176176.955049213233.121462644292.465164194
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -7 through 366)AA-7 - 3661 - 373
22chain 'B' and (resid 2 through 367 )BB2 - 3671 - 366
33chain 'D' and (resid 465 through 654)DG465 - 6541 - 176
44chain 'E' and (resid -1 through 366 )EC-1 - 3661 - 367
55chain 'F' and (resid -1 through 366 )FD-1 - 3661 - 367
66chain 'Y' and (resid 464 through 654 )YE464 - 6541 - 186
77chain 'Z' and (resid 465 through 656 )ZF465 - 6562 - 187

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