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- PDB-3gf0: Bifunctional dCTP deaminase-dUTPase mutant enzyme variant E145Q f... -

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Basic information

Entry
Database: PDB / ID: 3gf0
TitleBifunctional dCTP deaminase-dUTPase mutant enzyme variant E145Q from Methanocaldococcus jannaschii in complex with pyrophosphate and magnesium
ComponentsdCTP deaminase, dUMP-forming
KeywordsHYDROLASE / dCTP deaminase-dUTPase / bifunctional hydrolase / magnesium / nucleotide metabolism
Function / homology
Function and homology information


dCTP deaminase (dUMP-forming) / dCTP deaminase (dUMP-forming) activity / dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / nucleotide binding
Similarity search - Function
dCTP deaminase / dCTP deaminase-like / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
PYROPHOSPHATE 2- / dCTP deaminase, dUMP-forming
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.62 Å
AuthorsSiggaard, J.H.B. / Johansson, E. / Vognsen, T. / Helt, S.S. / Harris, P. / Willemoes, M.
CitationJournal: To be Published
Title: Pre-steady State Kinetic and Structural Evidence for a Concerted Biofunctionality in dCTP deaminase-dUTPase from Methanocaldococcus jannaschii
Authors: Siggaard, J.H.B. / Johansson, E. / Vognsen, T. / Helt, S.S. / Harris, P. / Larsen, S. / Willemoes, M.
History
DepositionFeb 26, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionMar 10, 2009ID: 2HXE
Revision 1.0Mar 10, 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 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 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

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Assembly

Deposited unit
A: dCTP deaminase, dUMP-forming
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7346
Polymers23,4611
Non-polymers2735
Water1,29772
1
A: dCTP deaminase, dUMP-forming
hetero molecules

A: dCTP deaminase, dUMP-forming
hetero molecules

A: dCTP deaminase, dUMP-forming
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,20218
Polymers70,3833
Non-polymers82015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
Buried area14340 Å2
ΔGint-179 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.569, 171.569, 171.569
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-278-

HOH

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Components

#1: Protein dCTP deaminase, dUMP-forming / Bifunctional deaminase/diphosphatase / MjDCD-DUT / DCD/DUT


Mass: 23460.869 Da / Num. of mol.: 1 / Mutation: E145Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q57872, dCTP deaminase (dUMP-forming)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 4.48 Å3/Da / Density % sol: 72.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 20% PEG3350, 0.2M TRIPOTASSIUM CITRATE , pH 8.30, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 23, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.62→25 Å / Num. obs: 14787 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.101 / Net I/σ(I): 26.8
Reflection shellResolution: 2.62→2.69 Å / Mean I/σ(I) obs: 5.4 / Rsym value: 0.434 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2HXB

2hxb


Resolution: 2.62→24.26 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.133 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.284 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22922 636 4.8 %RANDOM
Rwork0.19054 ---
all0.19235 14787 --
obs0.19235 12634 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.679 Å2
Refinement stepCycle: LAST / Resolution: 2.62→24.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 13 72 1756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221718
X-RAY DIFFRACTIONr_angle_refined_deg1.9761.9722330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.25204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39724.68479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53615310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.395156
X-RAY DIFFRACTIONr_chiral_restr0.1210.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211276
X-RAY DIFFRACTIONr_mcbond_it1.1041.51019
X-RAY DIFFRACTIONr_mcangle_it2.23821667
X-RAY DIFFRACTIONr_scbond_it3.6383699
X-RAY DIFFRACTIONr_scangle_it6.0814.5663
LS refinement shellResolution: 2.619→2.687 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 40 -
Rwork0.231 914 -
obs--99.9 %

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