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- PDB-1q5u: HUMAN DUTP PYROPHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 1q5u
TitleHUMAN DUTP PYROPHOSPHATASE
ComponentsdUTP pyrophosphatase
KeywordsHYDROLASE / DNA REPAIR / ENZYME-DNA INTERACTIONS
Function / homology
Function and homology information


pyrimidine deoxyribonucleotide binding / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / peroxisome proliferator activated receptor binding / nucleobase-containing compound metabolic process / signaling receptor inhibitor activity / dTMP biosynthetic process ...pyrimidine deoxyribonucleotide binding / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / peroxisome proliferator activated receptor binding / nucleobase-containing compound metabolic process / signaling receptor inhibitor activity / dTMP biosynthetic process / regulation of protein-containing complex assembly / liver development / DNA replication / magnesium ion binding / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus
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, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMol, C.D. / Harris, J.M. / Mcintosh, E.M. / Tainer, J.A.
CitationJournal: Structure / Year: 1996
Title: Human dUTP Pyrophosphatase: Uracil Recognition by a Beta Hairpin and Active Sites Formed by Three Separate Subunits
Authors: Mol, C.D. / Harris, J.M. / Mcintosh, E.M. / Tainer, J.A.
History
DepositionAug 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: dUTP pyrophosphatase
Y: dUTP pyrophosphatase
Z: dUTP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)48,7333
Polymers48,7333
Non-polymers00
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9800 Å2
ΔGint-47 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.991, 110.666, 52.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsthe asymmetric unit contains the biologically-relevant trimer.

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Components

#1: Protein dUTP pyrophosphatase


Mass: 16244.277 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDUT / Plasmid: PEM409 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33316
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.1M sodium citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
220 mMHEPES1droppH7.5
3100 mM1dropNaCl
41.0-1.2 Msodium citrate1reservoirpH8.0
5100 mMimidazole/malate1reservoirpH7.5-8.5

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 3, 1995 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 29007 / Num. obs: 29007 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 8.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2900 / Rsym value: 0.453 / % possible all: 98.9
Reflection
*PLUS
% possible obs: 97 % / Num. measured all: 101047
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DUP

1dup


Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.617 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.188 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22582 1467 5.1 %RANDOM
Rwork0.1878 ---
all0.18965 27503 --
obs0.18965 27503 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.244 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2---0.67 Å20 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3057 0 0 304 3361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213127
X-RAY DIFFRACTIONr_angle_refined_deg0.9871.9464224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8215387
X-RAY DIFFRACTIONr_chiral_restr0.0690.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022425
X-RAY DIFFRACTIONr_nbd_refined0.1680.21050
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.223
X-RAY DIFFRACTIONr_mcbond_it0.3741.51932
X-RAY DIFFRACTIONr_mcangle_it0.74623087
X-RAY DIFFRACTIONr_scbond_it1.2131195
X-RAY DIFFRACTIONr_scangle_it2.0614.51137
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.316 96
Rwork0.256 2040
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.71870.21010.43161.1590.37853.2333-0.0170.0904-0.0317-0.2032-0.06390.1547-0.0059-0.22530.08090.10060.0102-0.02820.08340.01440.0626.54836.9858.317
22.0099-0.9885-0.10241.9710.03580.9869-0.0217-0.0057-0.09490.0079-0.00340.07230.0005-0.0530.02520.0233-0.0020.00190.0484-0.01290.005615.48224.22619.556
31.32940.12060.05061.51490.33880.9930.01070.02670.1078-0.1210.00910.0349-0.1143-0.0327-0.01970.04580.0069-0.00090.05250.00510.030714.04643.10124.833
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1XA-2 - 1284 - 134
2X-RAY DIFFRACTION2YB0 - 1266 - 132
3X-RAY DIFFRACTION3ZC-5 - 1261 - 132
Refinement
*PLUS
Highest resolution: 2 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.78

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