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- PDB-5e5c: Crystal structure of dihydropyrimidinase from Pseudomonas aerugin... -

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Basic information

Entry
Database: PDB / ID: 5e5c
TitleCrystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1
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
D-hydantoinase/dihydropyrimidinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHuang, C.C. / Huang, Y.H. / Hsieh, Y.C. / Tzeng, C.T. / Chen, C.J. / Huang, C.Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1: Insights into the molecular basis of formation of a dimer
Authors: Tzeng, C.T. / Huang, Y.H. / Huang, C.Y.
History
DepositionOct 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,5516
Polymers106,2892
Non-polymers2624
Water6,089338
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-167 kcal/mol
Surface area31630 Å2
2
A: D-hydantoinase/dihydropyrimidinase
C: D-hydantoinase/dihydropyrimidinase
hetero molecules

A: D-hydantoinase/dihydropyrimidinase
C: D-hydantoinase/dihydropyrimidinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,10212
Polymers212,5794
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area13020 Å2
ΔGint-327 kcal/mol
Surface area58310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.134, 112.134, 161.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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 (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: dht, PA0441 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I676, dihydropyrimidinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.27 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: 10% PEG8000, 100mM HEPES sodium salt, 200mM Calcium Acetate

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.1→97.11 Å / Num. all: 68937 / Num. obs: 68799 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 19.21
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.976 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FTW

2ftw


Resolution: 2.1→97.11 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.515 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21546 3471 5.1 %RANDOM
Rwork0.16957 ---
obs0.17191 65158 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.554 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å2-0 Å2
2---0.03 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.1→97.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7356 0 4 338 7698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0197540
X-RAY DIFFRACTIONr_bond_other_d0.0010.027029
X-RAY DIFFRACTIONr_angle_refined_deg1.8791.94210254
X-RAY DIFFRACTIONr_angle_other_deg0.9316115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.435955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99523.086350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.662151147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9211562
X-RAY DIFFRACTIONr_chiral_restr0.1170.21113
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021819
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4462.7413826
X-RAY DIFFRACTIONr_mcbond_other2.4422.743825
X-RAY DIFFRACTIONr_mcangle_it3.3834.1024779
X-RAY DIFFRACTIONr_mcangle_other3.3834.1034780
X-RAY DIFFRACTIONr_scbond_it3.4093.1173714
X-RAY DIFFRACTIONr_scbond_other3.4083.1173715
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1034.5355476
X-RAY DIFFRACTIONr_long_range_B_refined6.34422.6448899
X-RAY DIFFRACTIONr_long_range_B_other6.32522.5738778
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 230 -
Rwork0.249 4716 -
obs--97.57 %

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