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- PDB-3a6s: Crystal structure of the MutT protein -

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Basic information

Entry
Database: PDB / ID: 3a6s
TitleCrystal structure of the MutT protein
ComponentsMutator mutT protein
KeywordsHYDROLASE / ALPHA-BETA-ALPHA SANDWICH / DNA DAMAGE / DNA REPAIR / DNA REPLICATION / MUTATOR PROTEIN
Function / homology
Function and homology information


dGDP catabolic process / 8-oxo-dGTP diphosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / nucleotide-excision repair / manganese ion binding / DNA replication ...dGDP catabolic process / 8-oxo-dGTP diphosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / nucleotide-excision repair / manganese ion binding / DNA replication / DNA repair / magnesium ion binding
Similarity search - Function
Mutator MutT / : / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain ...Mutator MutT / : / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / 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
L(+)-TARTARIC ACID / 8-oxo-dGTP diphosphatase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsNakamura, T. / Yamagata, Y.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base
Authors: Nakamura, T. / Meshitsuka, S. / Kitagawa, S. / Abe, N. / Yamada, J. / Ishino, T. / Nakano, H. / Tsuzuki, T. / Doi, T. / Kobayashi, Y. / Fujii, S. / Sekiguchi, M. / Yamagata, Y.
History
DepositionSep 9, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0634
Polymers29,8902
Non-polymers1732
Water3,423190
1
A: Mutator mutT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9682
Polymers14,9451
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mutator mutT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0952
Polymers14,9451
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-20 kcal/mol
Surface area12220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.902, 71.608, 55.797
Angle α, β, γ (deg.)90.00, 99.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mutator mutT protein / 7 / 8-dihydro-8-oxoguanine-triphosphatase / 8-oxo-dGTPase / dGTP pyrophosphohydrolase


Mass: 14945.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: mutT / Plasmid: PET8C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P08337, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M POTASSIUM SODIUM TARTRATE, 87mM HEPES, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU10.708
SYNCHROTRONPhoton Factory BL-18B20.9791, 0.9793, 0.9500
SYNCHROTRONSPring-8 BL44XU30.9795, 0.9797, 0.9500
Detector
TypeIDDetectorDate
MARRESEARCH1CCDOct 28, 1999
ADSC QUANTUM 42CCDOct 20, 2001
OXFORD PX2103CCDJun 19, 2001
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
3MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.7081
20.97911
30.97931
40.951
50.97951
60.97971
ReflectionResolution: 1.8→20 Å / Num. obs: 24217 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 15.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 7.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→19.81 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 848528.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2399 9.9 %RANDOM
Rwork0.204 ---
obs0.204 24213 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.91 Å2 / ksol: 0.44 e/Å3
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20.67 Å2
2--2.15 Å20 Å2
3----2.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 11 190 2226
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.42.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 382 9.9 %
Rwork0.213 3493 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TLA.PARAMTLA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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