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- PDB-9kce: Crystal Structure of the ATP analog-bound closed state of Thermot... -

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Basic information

Entry
Database: PDB / ID: 9kce
TitleCrystal Structure of the ATP analog-bound closed state of Thermotoga maritima MutS2
ComponentsEndonuclease MutS2
KeywordsDNA BINDING PROTEIN / ATPase / MutS family / MutS2 / homologous recombination
Function / homology
Function and homology information


mismatched DNA binding / negative regulation of DNA recombination / ATP-dependent DNA damage sensor activity / ribosomal large subunit binding / mismatch repair / rescue of stalled ribosome / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-stranded DNA binding / endonuclease activity / Hydrolases; Acting on ester bonds ...mismatched DNA binding / negative regulation of DNA recombination / ATP-dependent DNA damage sensor activity / ribosomal large subunit binding / mismatch repair / rescue of stalled ribosome / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-stranded DNA binding / endonuclease activity / Hydrolases; Acting on ester bonds / rRNA binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
Endonuclease MutS2 / MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Smr domain / Small MutS-related domain / Smr domain superfamily / Smr domain / Smr domain profile. / DNA mismatch repair MutS family / DNA mismatch repair protein MutS, C-terminal ...Endonuclease MutS2 / MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Smr domain / Small MutS-related domain / Smr domain superfamily / Smr domain / Smr domain profile. / DNA mismatch repair MutS family / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core / DNA mismatch repair protein MutS, core domain superfamily / MutS domain V / DNA mismatch repair proteins mutS family signature. / DNA-binding domain of DNA mismatch repair MUTS family / ATPase domain of DNA mismatch repair MUTS family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Endonuclease MutS2
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsFukui, K. / Murakawa, T. / Yano, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K08718 Japan
CitationJournal: Structure / Year: 2025
Title: ATP binding controls the molecular function of bacterial MutS2 by mediating closure of the dimeric clamp structure.
Authors: Fukui, K. / Murakawa, T. / Hino, N. / Kondo, N. / Yano, T.
History
DepositionNov 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Endonuclease MutS2
C: Endonuclease MutS2
A: Endonuclease MutS2
D: Endonuclease MutS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,01126
Polymers226,5484
Non-polymers3,46322
Water3,387188
1
B: Endonuclease MutS2
C: Endonuclease MutS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,10414
Polymers113,2742
Non-polymers1,83012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9400 Å2
ΔGint-182 kcal/mol
Surface area40670 Å2
MethodPISA
2
A: Endonuclease MutS2
D: Endonuclease MutS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,90712
Polymers113,2742
Non-polymers1,63310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9510 Å2
ΔGint-145 kcal/mol
Surface area41090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.740, 142.850, 139.420
Angle α, β, γ (deg.)90.000, 105.390, 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

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Protein , 1 types, 4 molecules BCAD

#1: Protein
Endonuclease MutS2


Mass: 56637.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: mutS2, mutSB, TM_1278 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q9X105, Hydrolases; Acting on ester bonds

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Non-polymers , 5 types, 210 molecules

#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Sodium citrate tribasic dihydrate, 1.0M Ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→48.95 Å / Num. obs: 98583 / % possible obs: 99.9 % / Redundancy: 16.2 % / Biso Wilson estimate: 36.86 Å2 / CC1/2: 0.989 / Net I/σ(I): 6.26
Reflection shellResolution: 2.49→2.66 Å / Redundancy: 15 % / Mean I/σ(I) obs: 0.98 / Num. unique obs: 17668 / CC1/2: 0.795 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487model building
XDSdata reduction
XDSdata scaling
Coot0.9.8.92model building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→48.95 Å / SU ML: 0.3047 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.8379
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2644 1681 1.71 %
Rwork0.2207 96831 -
obs0.2214 98512 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.84 Å2
Refinement stepCycle: LAST / Resolution: 2.49→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15127 0 199 188 15514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004115605
X-RAY DIFFRACTIONf_angle_d0.693521197
X-RAY DIFFRACTIONf_chiral_restr0.04572471
X-RAY DIFFRACTIONf_plane_restr0.00572707
X-RAY DIFFRACTIONf_dihedral_angle_d17.79295774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.560.32741370.28338024X-RAY DIFFRACTION99.84
2.56-2.650.35161400.28698038X-RAY DIFFRACTION99.9
2.65-2.740.29581390.26918064X-RAY DIFFRACTION99.95
2.74-2.850.34181440.27338030X-RAY DIFFRACTION99.9
2.85-2.980.31821400.26898083X-RAY DIFFRACTION99.87
2.98-3.140.31631370.25958018X-RAY DIFFRACTION99.9
3.14-3.330.30331380.23928036X-RAY DIFFRACTION99.93
3.33-3.590.23251390.22078081X-RAY DIFFRACTION99.98
3.59-3.950.24411410.20838071X-RAY DIFFRACTION99.96
3.95-4.520.22711370.18048090X-RAY DIFFRACTION99.98
4.52-5.70.21681430.1918107X-RAY DIFFRACTION99.98
5.7-48.950.24741460.18998189X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: 5.5282781862 Å / Origin y: 40.1690783676 Å / Origin z: -32.1554348895 Å
111213212223313233
T0.598381024152 Å20.00451303318767 Å2-0.188766840722 Å2-0.388670062384 Å2-0.0630681159095 Å2--0.311312817264 Å2
L-0.0452881928905 °20.0428843273455 °20.244477513878 °2-0.222984008396 °20.211996655266 °2--0.678000581195 °2
S-0.0106330954633 Å °-0.0124992269824 Å °-0.0274807153454 Å °-0.0650891936393 Å °0.0130981096026 Å °0.00173337602769 Å °0.0173894339369 Å °0.19237152694 Å °-0.0294980768931 Å °
Refinement TLS groupSelection details: all

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