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- PDB-4lhr: Crystal structure of a deoxyuridine 5'-triphosphate nucleotidohyd... -

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Basic information

Entry
Database: PDB / ID: 4lhr
TitleCrystal structure of a deoxyuridine 5'-triphosphate nucleotidohydrolase from Burkholderia thailandensis
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / nucleotide metabolism / pyrimidine
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a deoxyuridine 5'-triphosphate nucleotidohydrolase from Burkholderia thailandensis
Authors: Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionJul 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0262
Polymers16,8311
Non-polymers1941
Water2,936163
1
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0776
Polymers50,4943
Non-polymers5833
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area11140 Å2
ΔGint-44 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.360, 84.360, 54.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Deoxyuridine 5'-triphosphate nucleotidohydrolase / dUTPase / dUTP pyrophosphatase


Mass: 16831.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I0767, dut / Production host: Escherichia coli (E. coli) / References: UniProt: Q2T0H6, dUTP diphosphatase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: ButhA.00115.a.B1.PW37235 at 35.5 mg/mL against JCSG+ C6, 40% PEG 300, 0.1 M phosphate-citrate pH 4.2, crystal tracking ID 242052c6, unique puck ID ozx5-6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 35554 / Num. obs: 35545 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 15.3 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 34.27
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.5-1.540.4545.021100
1.54-1.580.3656.151100
1.58-1.630.2857.821100
1.63-1.680.2379.321100
1.68-1.730.2511.981100
1.73-1.790.21616.811100
1.79-1.860.16821.661100
1.86-1.940.12927.411100
1.94-2.020.08935.661100
2.02-2.120.07740.211100
2.12-2.240.06745.981100
2.24-2.370.05950.191100
2.37-2.540.04957.931100
2.54-2.740.04464.711100
2.74-30.0468.31199.9
3-3.350.03677.041100
3.35-3.870.03480.961100
3.87-4.740.03183.84199.9
4.74-6.710.02984.051100
6.710.02677.77197.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.2 Å43.75 Å
Translation3.2 Å43.75 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1eu5

1eu5


Resolution: 1.5→43.78 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.262 / SU ML: 0.022 / SU R Cruickshank DPI: 0.0423 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13471 1778 5 %RANDOM
Rwork0.11718 ---
obs0.11805 33748 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.149 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.06 Å2-0 Å2
2--0.06 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1006 0 13 163 1182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191126
X-RAY DIFFRACTIONr_bond_other_d0.0010.021139
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9991549
X-RAY DIFFRACTIONr_angle_other_deg0.73632625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7255159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69323.11145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02915189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.038159
X-RAY DIFFRACTIONr_chiral_restr0.0870.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211277
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02248
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5561.544561
X-RAY DIFFRACTIONr_mcbond_other1.4571.54560
X-RAY DIFFRACTIONr_mcangle_it2.0192.326706
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1731.925565
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.26232264
X-RAY DIFFRACTIONr_sphericity_free30.54550
X-RAY DIFFRACTIONr_sphericity_bonded8.13452345
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.144 127 -
Rwork0.132 2466 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 30.7285 Å / Origin y: -27.7218 Å / Origin z: 13.5647 Å
111213212223313233
T0.0117 Å2-0.0092 Å2-0.0017 Å2-0.0274 Å20.0175 Å2--0.0158 Å2
L0.4187 °20.156 °2-0.0336 °2-0.2594 °2-0.0055 °2--0.3233 °2
S0.0213 Å °0.0157 Å °0.0039 Å °0.0157 Å °0.0314 Å °0.0324 Å °0.0304 Å °-0.0857 Å °-0.0526 Å °

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