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

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Basic information

Entry
Database: PDB / ID: 6mao
TitleCrystal structure of Deoxyuridine 5'-triphosphate nucleotidohydrolase from Legionella pneumophila Philadelphia 1 in complex with dUMP (Deoxyuridine 5'-monophosphate)
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
2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 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)17,9144
Polymers17,3921
Non-polymers5223
Water2,414134
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)53,74312
Polymers52,1753
Non-polymers1,5679
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 area13110 Å2
ΔGint-123 kcal/mol
Surface area16220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.670, 85.670, 55.460
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-427-

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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5ZSN0, dUTP diphosphatase
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.38 Å3/Da / Density % sol: 63.6 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Molecular Dimensions Morpheus screen, condition C4: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 30mM each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate: 100mM ...Details: Molecular Dimensions Morpheus screen, condition C4: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 30mM each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate: 100mM MES/imidazole pH 6.5: LepnA.01206.a.B1.PS38438 at 24.33mg/ml: 2h soak with 5mM MgCl2 + dUTP with was converted to dUMP: cryo: direct: 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: 1.95→37.096 Å / Num. obs: 17033 / % possible obs: 100 % / Redundancy: 9.282 % / Biso Wilson estimate: 34.444 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.063 / Χ2: 1.044 / Net I/σ(I): 22.98
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-25.220.473.0412650.8780.52399.9
2-2.066.2160.3594.612050.9440.392100
2.06-2.126.9390.3026.1211760.9570.327100
2.12-2.187.6590.2887.0511540.9690.309100
2.18-2.258.1670.2279.1911290.9830.242100
2.25-2.338.7230.20510.3410740.9890.218100
2.33-2.429.5620.17412.8410370.9920.184100
2.42-2.5210.8340.14216.6410190.9960.149100
2.52-2.6311.0460.1219.419610.9960.126100
2.63-2.7611.0760.09922.629370.9980.103100
2.76-2.9111.0510.08625.478790.9980.0999.9
2.91-3.0811.060.07130.718210.9980.075100
3.08-3.311.0670.05737.97950.9990.06100
3.3-3.5610.980.04846.067170.9990.05100
3.56-3.910.7840.04251.56860.9990.044100
3.9-4.3610.8770.03756.66030.9990.039100
4.36-5.0310.8280.03161.245480.9980.033100
5.03-6.1710.9720.03160.034620.9990.03399.8
6.17-8.7210.9360.03156.623600.9990.032100
8.72-37.09610.2980.02464.5720510.02598.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.14_3211)refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo structure, 6MAI

6mai


Resolution: 1.95→37.096 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.43
RfactorNum. reflection% reflection
Rfree0.1811 1774 10.42 %
Rwork0.1482 --
obs0.1515 17031 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.86 Å2 / Biso mean: 34.5277 Å2 / Biso min: 14.22 Å2
Refinement stepCycle: final / Resolution: 1.95→37.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 33 138 1215
Biso mean--62.52 45.37 -
Num. residues----137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091126
X-RAY DIFFRACTIONf_angle_d0.9331547
X-RAY DIFFRACTIONf_dihedral_angle_d13.83689
X-RAY DIFFRACTIONf_chiral_restr0.074184
X-RAY DIFFRACTIONf_plane_restr0.006205
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.95-2.00280.25211360.210411791315
2.0028-2.06170.22771290.180111561285
2.0617-2.12820.20211460.17811581304
2.1282-2.20430.18521540.162811481302
2.2043-2.29250.18791200.156811711291
2.2925-2.39680.20361280.161511801308
2.3968-2.52320.22521590.161411511310
2.5232-2.68120.19611330.153711771310
2.6812-2.88820.1871190.163211711290
2.8882-3.17870.20621230.16412011324
3.1787-3.63830.18711260.139411801306
3.6383-4.58250.14381500.11611751325
4.5825-37.10290.15551510.136512101361
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)
18.84120.6294-6.14842.0796-0.424.2766-0.1591-0.9190.24570.42480.0813-0.05020.30090.41450.0420.2504-0.0567-0.04230.5094-0.04280.2722-24.427228.794716.6315
28.7081.60830.30212.5066-1.33521.0526-0.04660.2590.694-0.09980.1469-0.0707-0.28720.4859-0.11180.304-0.1385-0.03140.3761-0.04580.2778-24.374937.18468.0661
34.79053.4479-6.74365.8484-4.49589.7272-0.12330.12960.403-0.06030.1328-0.51560.45780.6232-0.13410.191-0.0395-0.02550.4485-0.01560.2529-24.409934.5831-1.0255
44.1356-0.42523.67130.9344-0.27343.2823-0.17640.49480.0582-0.10680.0992-0.1668-0.19910.69040.06270.2173-0.04380.03310.3414-0.03340.2388-27.222327.537-4.7203
52.2404-0.37981.26731.243-0.59693.70290.02940.00070.1040.0677-0.0142-0.0958-0.00110.12970.0130.1472-0.0252-0.00320.1785-0.01450.1898-34.167726.56834.1699
62.29680.3477-0.57831.51220.03622.9120.04030.19280.143-0.12660.0475-0.0951-0.29540.4442-0.04910.1556-0.04280.01120.1996-0.00570.1832-33.018632.0771-4.3328
77.94085.11150.36233.48150.37323.29310.4825-0.7007-0.11890.7984-0.40720.46240.4454-0.5371-0.01340.3653-0.03170.040.27150.09280.3767-50.00486.449317.2032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 9 )A2 - 9
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 29 )A10 - 29
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 40 )A30 - 40
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 58 )A41 - 58
5X-RAY DIFFRACTION5chain 'A' and (resid 59 through 97 )A59 - 97
6X-RAY DIFFRACTION6chain 'A' and (resid 98 through 124 )A98 - 124
7X-RAY DIFFRACTION7chain 'A' and (resid 125 through 138 )A125 - 138

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