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- PDB-3fk9: Crystal structure of mMutator MutT protein from Bacillus halodurans -

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Basic information

Entry
Database: PDB / ID: 3fk9
TitleCrystal structure of mMutator MutT protein from Bacillus halodurans
ComponentsMutator MutT protein
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / metal ion binding
Similarity search - Function
NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Mutator MutT protein
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Hu, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of mMutator MutT protein from Bacillus halodurans
Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Hu, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionDec 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mutator MutT protein
B: Mutator MutT protein


Theoretical massNumber of molelcules
Total (without water)43,5922
Polymers43,5922
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-12 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.345, 59.084, 108.357
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsdimer

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Components

#1: Protein Mutator MutT protein


Mass: 21796.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: BH3570 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K704
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 100mM MES pH 6.5, 20% PEG 10K, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 8, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 12601 / Num. obs: 12551 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 54.2 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 12.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 4.5 / Num. measured all: 10162 / Num. unique all: 1778 / Rsym value: 0.279 / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.5→10 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.292 / WRfactor Rwork: 0.361 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.767 / SU B: 10.806 / SU ML: 0.237 / SU R Cruickshank DPI: 0.659 / SU Rfree: 0.343 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.659 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.293 642 5.2 %RANDOM
Rwork0.222 ---
obs0.226 12287 99.35 %-
all-12367 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 81.52 Å2 / Biso mean: 58.37 Å2 / Biso min: 38.34 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20 Å20 Å2
2---1.48 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 0 5 2457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222522
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9543425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72424.414111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.41215429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.105159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211899
X-RAY DIFFRACTIONr_mcbond_it0.7281.51522
X-RAY DIFFRACTIONr_mcangle_it1.39622450
X-RAY DIFFRACTIONr_scbond_it1.99531000
X-RAY DIFFRACTIONr_scangle_it3.3644.5975
LS refinement shellResolution: 2.5→2.561 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 39 -
Rwork0.295 793 -
all-832 -
obs-793 98.93 %

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