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- PDB-9ixo: Crystal structure of OXA-14 -

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Basic information

Entry
Database: PDB / ID: 9ixo
TitleCrystal structure of OXA-14
ComponentsBeta-lactamase
KeywordsHYDROLASE / Class D Beta-lactamase / OXA-14 / OXA-10 variant
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLee, C.E. / Park, Y.S. / Park, H.J. / Kang, L.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2017M3A9E4078017 Korea, Republic Of
CitationJournal: Emerg Microbes Infect / Year: 2024
Title: Structural insights into alterations in the substrate spectrum of serine-beta-lactamase OXA-10 from Pseudomonas aeruginosa by single amino acid substitutions.
Authors: Lee, C.E. / Park, Y. / Park, H. / Kwak, K. / Lee, H. / Yun, J. / Lee, D. / Lee, J.H. / Lee, S.H. / Kang, L.W.
History
DepositionJul 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)55,7892
Polymers55,7892
Non-polymers00
Water9,350519
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-11 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.323, 102.627, 126.421
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase


Mass: 27894.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: OXA-14 / Plasmid: pET-29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q59648, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2 M Sodium formate, 0.1 M Tris-HCl pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Steady flow of liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→33.89 Å / Num. obs: 51961 / % possible obs: 97.17 % / Redundancy: 9.4 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.025 / Rrim(I) all: 0.08 / Net I/σ(I): 17.06
Reflection shellResolution: 1.86→1.93 Å / Rmerge(I) obs: 0.479 / Num. unique obs: 4841

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FOF

1fof


Resolution: 1.86→33.89 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.432 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22052 2633 5.1 %RANDOM
Rwork0.17609 ---
obs0.17837 49328 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.116 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.86→33.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 0 0 519 4435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124031
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163831
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.6325452
X-RAY DIFFRACTIONr_angle_other_deg0.531.5668845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.675518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54410718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02926
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_it2.462.5511989
X-RAY DIFFRACTIONr_mcbond_other2.462.5511989
X-RAY DIFFRACTIONr_mcangle_it3.6464.5712488
X-RAY DIFFRACTIONr_mcangle_other3.6454.5722489
X-RAY DIFFRACTIONr_scbond_it3.1962.8812042
X-RAY DIFFRACTIONr_scbond_other3.1952.8812043
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9915.1232965
X-RAY DIFFRACTIONr_long_range_B_refined7.66927.355013
X-RAY DIFFRACTIONr_long_range_B_other7.27625.94840
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.863→1.911 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 192 -
Rwork0.281 3297 -
obs--89.99 %

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