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- PDB-7e3u: Crystal structure of the Pseudomonas aeruginosa dihydropyrimidina... -

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Basic information

Entry
Database: PDB / ID: 7e3u
TitleCrystal structure of the Pseudomonas aeruginosa dihydropyrimidinase complexed with 5-AU
ComponentsD-hydantoinase/dihydropyrimidinase
KeywordsHYDROLASE / dihydropyrimidinase
Function / homology
Function and homology information


dihydropyrimidinase / dihydropyrimidinase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / metal ion binding / cytosol
Similarity search - Function
Hydantoinase/dihydropyrimidinase / : / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
5-AMINO-1H-PYRIMIDINE-2,4-DIONE / D-hydantoinase/dihydropyrimidinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.159 Å
AuthorsYang, Y.C. / Luo, R.H. / Huang, Y.H. / Huang, C.Y. / Lin, E.S.
CitationJournal: Bioinorg Chem Appl / Year: 2022
Title: Molecular Insights into How the Dimetal Center in Dihydropyrimidinase Can Bind the Thymine Antagonist 5-Aminouracil: A Different Binding Mode from the Anticancer Drug 5-Fluorouracil.
Authors: Lin, E.S. / Luo, R.H. / Yang, Y.C. / Huang, C.Y.
History
DepositionFeb 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-hydantoinase/dihydropyrimidinase
B: D-hydantoinase/dihydropyrimidinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0207
Polymers104,6322
Non-polymers3895
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-171 kcal/mol
Surface area31570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.667, 112.667, 161.432
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-710-

HOH

21A-861-

HOH

31B-752-

HOH

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Components

#1: Protein D-hydantoinase/dihydropyrimidinase / DHPase


Mass: 52315.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: dht, PA0441
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9I676, dihydropyrimidinase
#2: Chemical ChemComp-WBU / 5-AMINO-1H-PYRIMIDINE-2,4-DIONE


Mass: 127.101 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 16%PEG8000, 100mM HEPES pH7.5, 200mM Calcium Acetate

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.159→30 Å / Num. obs: 64183 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 3.1
Reflection shellResolution: 2.159→2.24 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 23.7 / Num. unique obs: 6340 / CC1/2: 0.866 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E5C

5e5c


Resolution: 2.159→28.012 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2301 3164 4.93 %
Rwork0.1864 60954 -
obs0.1885 64118 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.35 Å2 / Biso mean: 36.4665 Å2 / Biso min: 14.4 Å2
Refinement stepCycle: final / Resolution: 2.159→28.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7348 0 18 459 7825
Biso mean--51.3 37.9 -
Num. residues----956
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.159-2.19110.27451420.23372621100
2.1911-2.22530.2861360.242611100
2.2253-2.26180.27791500.23632607100
2.2618-2.30070.30911290.23452627100
2.3007-2.34260.3191220.22932639100
2.3426-2.38760.29771380.22662654100
2.3876-2.43630.28621580.22422576100
2.4363-2.48920.26861310.21922612100
2.4892-2.54710.27621690.21682591100
2.5471-2.61080.28441370.2142640100
2.6108-2.68130.26681460.2172615100
2.6813-2.76010.28181250.20942658100
2.7601-2.84910.25671390.21512632100
2.8491-2.95090.26451260.21392665100
2.9509-3.06890.24681260.20772639100
3.0689-3.20840.24361300.2112664100
3.2084-3.37720.26741480.20112641100
3.3772-3.58840.22181450.18372647100
3.5884-3.86490.19211230.16742692100
3.8649-4.25260.19891250.15632673100
4.2526-4.86520.18071440.12922703100
4.8652-6.1190.16951250.16372725100
6.119-28.0120.18041500.156282299

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