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

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Basic information

Entry
Database: PDB / ID: 5ykd
TitleCrystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1 at 2.17 angstrom resolution
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: 2.17 Å
AuthorsHuang, Y.H. / Huang, C.Y.
CitationJournal: Bioinorg Chem Appl / Year: 2018
Title: Structural Basis for pH-Dependent Oligomerization of Dihydropyrimidinase fromPseudomonas aeruginosaPAO1.
Authors: Cheng, J.H. / Huang, C.C. / Huang, Y.H. / Huang, C.Y.
History
DepositionOct 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _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
Revision 1.2Nov 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)209,78712
Polymers209,2634
Non-polymers5238
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-315 kcal/mol
Surface area65690 Å2
Unit cell
Length a, b, c (Å)108.912, 155.699, 235.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
D-hydantoinase/dihydropyrimidinase / DHPase


Mass: 52315.844 Da / Num. of mol.: 4
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 10% PEG 8000, 100 mM HEPES, 200 mM calcium acetate pH 5.9

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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: Dec 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.17→117.79 Å / Num. obs: 100197 / % possible obs: 99.82 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 15.13
Reflection shellResolution: 2.17→2.26 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E5C

5e5c


Resolution: 2.17→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.011 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.198 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23121 5328 5 %RANDOM
Rwork0.17595 ---
obs0.17875 100197 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.431 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å2-0 Å2
2---2.43 Å2-0 Å2
3---1.41 Å2
Refinement stepCycle: 1 / Resolution: 2.17→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14684 0 8 313 15005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01915052
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214032
X-RAY DIFFRACTIONr_angle_refined_deg1.651.94220468
X-RAY DIFFRACTIONr_angle_other_deg0.844332172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45751908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04723.161696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.185152288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9315124
X-RAY DIFFRACTIONr_chiral_restr0.0940.22220
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02117420
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023628
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_it2.7463.7467635
X-RAY DIFFRACTIONr_mcbond_other2.7463.7467636
X-RAY DIFFRACTIONr_mcangle_it3.5965.619540
X-RAY DIFFRACTIONr_mcangle_other3.5965.619541
X-RAY DIFFRACTIONr_scbond_it3.5174.1237416
X-RAY DIFFRACTIONr_scbond_other3.5174.1237417
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.096.03510929
X-RAY DIFFRACTIONr_long_range_B_refined6.12230.36517122
X-RAY DIFFRACTIONr_long_range_B_other6.12730.35917082
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 389 -
Rwork0.237 7331 -
obs--100 %

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