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- PDB-6mai: Crystal structure of Deoxyuridine 5'-triphosphate nucleotidohydro... -

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Basic information

Entry
Database: PDB / ID: 6mai
TitleCrystal structure of Deoxyuridine 5'-triphosphate nucleotidohydrolase from Legionella pneumophila Philadelphia 1
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Structural characterization of dUTPase from Legionella pneumophila
Authors: Nguyen, C.L. / Tramell, A.R. / Norman, J.O. / Abendroth, J. / Barrett, K.F. / Craig, J.K. / Edwards, T.E. / Lorimer, D.D. / McLaughlin, K.J.
History
DepositionAug 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 9, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year

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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)17,6405
Polymers17,3921
Non-polymers2484
Water3,405189
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)52,92015
Polymers52,1753
Non-polymers74512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area12170 Å2
ΔGint-20 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.650, 84.650, 55.700
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-466-

HOH

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Components

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


Mass: 17391.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: dut, lpg2487 / Plasmid: LepnA.01206.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZSN0, dUTP diphosphatase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.32 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG1 screen, condition A1: 20% PEG 8000, 100mM HEPES/NaOH pH 7.5: LepnA.01206.a.B1.PS38438 at 24.33mg/ml: cryo: 20% EG in two steps: tray 301633a1, puck PXP9-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→42.325 Å / Num. obs: 20693 / % possible obs: 97.7 % / Redundancy: 7.736 % / Biso Wilson estimate: 29.774 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.04 / Χ2: 1.033 / Net I/σ(I): 31.78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.854.9490.4713.1514040.8710.52590.4
1.85-1.94.9840.3744.0213850.9240.41792.5
1.9-1.955.0760.275.5614190.9560.395
1.95-2.015.2330.2127.213580.970.23595.1
2.01-2.085.330.15910.1113490.9860.17697.1
2.08-2.155.9690.13712.5513490.9890.1598.5
2.15-2.236.9110.1116.8712750.9930.11999.5
2.23-2.327.3840.0920.3712330.9960.09799.6
2.32-2.437.6960.0823.6312200.9970.08699.8
2.43-2.558.1810.06728.8611410.9980.07199.8
2.55-2.688.8550.05834.2610920.9980.06299.9
2.68-2.8510.2830.04942.7810370.9990.05299.9
2.85-3.0411.1160.04451.019790.9990.046100
3.04-3.2911.0510.03562.1190810.036100
3.29-3.611.0370.02874.9983510.0399.9
3.6-4.0311.0380.02581.8876910.026100
4.03-4.6510.9880.02191.8666510.02299.8
4.65-5.6910.990.0291.7257510.021100
5.69-8.0510.9420.02286.4744610.023100
8.05-42.32510.1340.01997.832540.9990.0297.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.14_3211)refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1euw

1euw


Resolution: 1.8→42.325 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.04
RfactorNum. reflection% reflectionSelection details
Rfree0.1768 2013 9.73 %0
Rwork0.154 ---
obs0.1562 20691 97.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.66 Å2 / Biso mean: 28.2452 Å2 / Biso min: 10.83 Å2
Refinement stepCycle: final / Resolution: 1.8→42.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 16 192 1248
Biso mean--47.54 41.87 -
Num. residues----137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081110
X-RAY DIFFRACTIONf_angle_d0.8931518
X-RAY DIFFRACTIONf_dihedral_angle_d11.033679
X-RAY DIFFRACTIONf_chiral_restr0.067184
X-RAY DIFFRACTIONf_plane_restr0.005197
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8002-1.84520.24971300.2281230136090
1.8452-1.89510.2651320.21121243137592
1.8951-1.95090.22921410.18091294143595
1.9509-2.01380.19891600.17041263142395
2.0138-2.08580.14551040.15411358146297
2.0858-2.16930.19591410.16341347148899
2.1693-2.2680.19331810.159213061487100
2.268-2.38760.19541450.157613631508100
2.3876-2.53720.20331320.159113891521100
2.5372-2.7330.19911630.153913441507100
2.733-3.0080.17521420.158413691511100
3.008-3.44310.19141410.144913771518100
3.4431-4.33730.15691400.130813941534100
4.3373-42.33670.13041610.149814011562100
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)
16.41431.63180.3582.4187-1.45521.21350.0753-0.07070.6359-0.02090.0733-0.0491-0.45640.5486-0.18520.264-0.1352-0.0260.2688-0.03630.2013-23.77936.77488.9188
21.2810.10870.46980.9421-0.09652.20750.02880.03920.04610.03990.0306-0.1054-0.05510.3373-0.05680.0993-0.02770.00160.1716-0.02020.1423-29.883327.5971.9933
32.00450.5814-0.46910.76390.11822.36170.02880.11320.1005-0.05440.0531-0.0228-0.3370.4471-0.06490.1331-0.0382-0.00120.1453-0.00260.1669-32.603131.4743-3.13
44.46371.4841-0.28696.80530.22432.54440.159-0.5243-0.42580.4139-0.15580.27410.5635-0.379-0.02560.3489-0.05450.00570.23210.08360.2062-49.53066.220217.9857
58.72013.4918-6.26115.3264-2.73744.63190.0991-0.52260.45910.3472-0.03130.14620.0110.36140.01650.1836-0.0468-0.06320.4147-0.05080.1991-23.978928.373717.4448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 29 )A10 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 97 )A30 - 97
3X-RAY DIFFRACTION3chain 'A' and (resid 98 through 124 )A98 - 124
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 138 )A125 - 138
5X-RAY DIFFRACTION5chain 'A' and (resid 2 through 9 )A2 - 9

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