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- PDB-6klk: Crystal structure of the Pseudomonas aeruginosa dihydropyrimidina... -

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Basic information

Entry
Database: PDB / ID: 6klk
TitleCrystal structure of the Pseudomonas aeruginosa dihydropyrimidinase complexed with 5-FU
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 hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-FLUOROURACIL / D-hydantoinase/dihydropyrimidinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.759 Å
AuthorsHuang, Y.H. / Chen, I.C. / Huang, C.Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Crystal structure of dihydropyrimidinase in complex with anticancer drug 5-fluorouracil.
Authors: Huang, Y.H. / Ning, Z.J. / Huang, C.Y.
History
DepositionJul 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_conn_type.id

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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)105,0237
Polymers104,6322
Non-polymers3925
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-165 kcal/mol
Surface area30950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.333, 111.333, 159.977
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-757-

HOH

21A-816-

HOH

31A-863-

HOH

41A-900-

HOH

51B-710-

HOH

61B-792-

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 (E. coli) / References: UniProt: Q9I676, dihydropyrimidinase
#2: Chemical ChemComp-URF / 5-FLUOROURACIL


Mass: 130.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3FN2O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 18%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: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.759→30 Å / Num. obs: 114045 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.8
Reflection shellResolution: 1.759→1.82 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.471 / Num. unique obs: 11296 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E5C

5e5c


Resolution: 1.759→27.833 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 5674 4.98 %
Rwork0.1852 108276 -
obs0.1866 113950 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.96 Å2 / Biso mean: 23.187 Å2 / Biso min: 10.3 Å2
Refinement stepCycle: final / Resolution: 1.759→27.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7348 0 16 567 7931
Biso mean--35.39 27.48 -
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 (%)
1.759-1.77880.32442133546100
1.7788-1.79970.25321783588100
1.7997-1.82170.29791763596100
1.8217-1.84470.26981843539100
1.8447-1.8690.27891583599100
1.869-1.89460.25941853611100
1.8946-1.92170.28781623581100
1.9217-1.95030.26051983604100
1.9503-1.98080.27281773555100
1.9808-2.01330.22871953570100
2.0133-2.0480.27142023580100
2.048-2.08520.22871783575100
2.0852-2.12530.26851883582100
2.1253-2.16870.22361643608100
2.1687-2.21580.22512063622100
2.2158-2.26730.22081723597100
2.2673-2.3240.24341913604100
2.324-2.38680.21841533621100
2.3868-2.4570.22011633619100
2.457-2.53620.23471863622100
2.5362-2.62680.21372213543100
2.6268-2.73190.23452033607100
2.7319-2.85610.21982043638100
2.8561-3.00650.23942073591100
3.0065-3.19460.21692043627100
3.1946-3.44090.19211743618100
3.4409-3.78640.17411883669100
3.7864-4.33250.17562143649100
4.3325-5.45180.14782220.1439366599

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