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- PDB-1q5h: Human dUTP Pyrophosphatase complex with dUDP -

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Basic information

Entry
Database: PDB / ID: 1q5h
TitleHuman dUTP Pyrophosphatase complex with dUDP
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'-DIPHOSPHATE / 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 7, 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 ...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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: dUTP pyrophosphatase
B: dUTP pyrophosphatase
C: dUTP pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9227
Polymers48,7333
Non-polymers1,1894
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint-68 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.197, 110.766, 53.243
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsthe crystallographic 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) / Plasmid: pEM409 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33316
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DUD / DEOXYURIDINE-5'-DIPHOSPHATE


Mass: 388.162 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N2O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.21 Å3/Da / Density % sol: 44.44 %
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: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 10, 1996 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 28406 / Num. obs: 28406 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.62 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 10.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2412 / Rsym value: 0.323 / % possible all: 82
Reflection
*PLUS
Num. measured all: 102902
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 82 %

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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: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.721 / SU ML: 0.103 / 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: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21426 1435 5.1 %RANDOM
Rwork0.17692 ---
all0.17877 26846 --
obs0.17877 26946 94.78 %-
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: 13.189 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2--0.85 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 73 238 3461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213294
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.9794458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8215402
X-RAY DIFFRACTIONr_chiral_restr0.0740.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022524
X-RAY DIFFRACTIONr_nbd_refined0.1660.21044
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2207
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.214
X-RAY DIFFRACTIONr_mcbond_it0.4021.51999
X-RAY DIFFRACTIONr_mcangle_it0.81123190
X-RAY DIFFRACTIONr_scbond_it1.4131295
X-RAY DIFFRACTIONr_scangle_it2.3844.51268
LS refinement shellResolution: 2.001→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.237 78
Rwork0.23 1673
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)
10.72210.18050.34071.2520.15033.0613-0.02290.1075-0.0295-0.2363-0.0470.13830.0073-0.20320.06990.10850.0073-0.03040.05260.01150.07857.14236.9587.937
22.6767-0.4864-0.04891.71250.25241.3252-0.03860.03510.0716-0.04290.01470.0504-0.0744-0.08330.02390.03720.0014-0.00350.0106-0.01230.034714.84225.98418.959
31.27590.1507-0.10292.10230.17191.27950.04220.03940.0515-0.1601-0.00650.0913-0.0875-0.0581-0.03570.04380.012-0.01320.03080.00010.056813.71541.48724.086
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1277 - 133
2X-RAY DIFFRACTION2BB1 - 1367 - 142
3X-RAY DIFFRACTION3CC-5 - 1361 - 142
Refinement
*PLUS
Highest resolution: 2 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.34

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