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- PDB-8wq9: Crystal structure of dihydropyrimidinase complexed with gamma-ami... -

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Basic information

Entry
Database: PDB / ID: 8wq9
TitleCrystal structure of dihydropyrimidinase complexed with gamma-aminobutyric acid
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
GAMMA-AMINO-BUTANOIC ACID / D-hydantoinase/dihydropyrimidinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsHuang, Y.H. / Huang, C.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: The complexed crystal structure of dihydropyrimidinase reveals a potential interactive link with the neurotransmitter gamma-aminobutyric acid (GABA).
Authors: Huang, Y.H. / Huang, C.Y.
History
DepositionOct 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,96410
Polymers106,2892
Non-polymers6748
Water12,953719
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-175 kcal/mol
Surface area32280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.314, 111.036, 112.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein D-hydantoinase/dihydropyrimidinase / DHPase


Mass: 53144.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: dht, PA0441 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9I676, dihydropyrimidinase
#2: Chemical
ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H9NO2 / 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.: 719 / 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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18%PEG8000, 100mM Tris-HCl pH7.0, 200mM Calcium Chloride

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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 315r / Detector: CCD / Date: Aug 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.96→30 Å / Num. obs: 75195 / % possible obs: 95.4 % / Redundancy: 3.4 % / CC1/2: 0.976 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 7479 / CC1/2: 0.921 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
PDB_EXTRACT3.27data extraction
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→27.74 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 3839 5.11 %
Rwork0.1711 --
obs0.1733 75156 94.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→27.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7348 0 32 719 8099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087556
X-RAY DIFFRACTIONf_angle_d0.96810268
X-RAY DIFFRACTIONf_dihedral_angle_d7.0571062
X-RAY DIFFRACTIONf_chiral_restr0.0581112
X-RAY DIFFRACTIONf_plane_restr0.011360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-1.990.30521350.23752141X-RAY DIFFRACTION78
1.99-2.020.28191490.21352648X-RAY DIFFRACTION97
2.02-2.050.2521450.20182668X-RAY DIFFRACTION97
2.05-2.080.23771640.19292646X-RAY DIFFRACTION97
2.08-2.110.26061460.18792679X-RAY DIFFRACTION97
2.11-2.140.25321380.18482681X-RAY DIFFRACTION97
2.14-2.170.20971380.18642694X-RAY DIFFRACTION97
2.18-2.210.23241460.18792689X-RAY DIFFRACTION97
2.21-2.250.25021640.18082611X-RAY DIFFRACTION97
2.25-2.30.26071510.1782676X-RAY DIFFRACTION97
2.3-2.340.23711440.17672659X-RAY DIFFRACTION97
2.34-2.390.23931330.18122694X-RAY DIFFRACTION97
2.39-2.450.22921280.17712698X-RAY DIFFRACTION97
2.45-2.510.21871420.17552661X-RAY DIFFRACTION96
2.51-2.580.22661250.17782669X-RAY DIFFRACTION96
2.58-2.650.20921410.17632669X-RAY DIFFRACTION96
2.65-2.740.23271590.182649X-RAY DIFFRACTION96
2.74-2.840.22611240.17892689X-RAY DIFFRACTION95
2.84-2.950.25091450.18432627X-RAY DIFFRACTION95
2.95-3.090.21741400.18432666X-RAY DIFFRACTION95
3.09-3.250.23941290.18712642X-RAY DIFFRACTION94
3.25-3.450.24131310.18142630X-RAY DIFFRACTION94
3.45-3.720.19091530.16412576X-RAY DIFFRACTION92
3.72-4.090.18641250.15342566X-RAY DIFFRACTION91
4.09-4.680.15351420.13432593X-RAY DIFFRACTION91
4.68-5.880.18271620.14952643X-RAY DIFFRACTION92
5.89-27.740.16481400.15492853X-RAY DIFFRACTION95

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