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- PDB-9ixr: Crystal structure of OXA-10 variant A124T in the complex with cef... -

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Basic information

Entry
Database: PDB / ID: 9ixr
TitleCrystal structure of OXA-10 variant A124T in the complex with ceftazidime
ComponentsBeta-lactamase OXA-10
KeywordsHYDROLASE / Class D Beta-lactamase / OXA-10 variant
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / periplasmic space / 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
Chem-CTJ / Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase OXA-10
B: Beta-lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7474
Polymers55,6472
Non-polymers1,0992
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-10 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.510, 99.040, 127.100
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 OXA-10 / Beta-lactamase PSE-2


Mass: 27823.662 Da / Num. of mol.: 2 / Mutation: A124T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla, oxa10, pse2 / Plasmid: pET-29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase
#2: Chemical ChemComp-CTJ / 1-({(2R)-2-[(1R)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}-2-oxoethyl]-4-carboxy-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyridinium


Mass: 549.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25N6O7S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.75 Å3/Da / Density % sol: 55.19 %
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: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.19→29.3 Å / Num. obs: 32211 / % possible obs: 99.61 % / Redundancy: 12.6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.042 / Rrim(I) all: 0.151 / Net I/σ(I): 15.63
Reflection shellResolution: 2.19→2.27 Å / Num. unique obs: 3169 / Rpim(I) all: 0.317

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FOF

1fof


Resolution: 2.19→29.3 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.167 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20926 1611 5 %RANDOM
Rwork0.1669 ---
obs0.16909 30601 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.067 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.19→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 0 0 228 4222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124086
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163868
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.6675524
X-RAY DIFFRACTIONr_angle_other_deg0.5991.5928916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.43516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49210722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024796
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02946
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_it3.7033.9621982
X-RAY DIFFRACTIONr_mcbond_other3.6913.961981
X-RAY DIFFRACTIONr_mcangle_it5.2577.1082474
X-RAY DIFFRACTIONr_mcangle_other5.2587.1112475
X-RAY DIFFRACTIONr_scbond_it4.8894.6072104
X-RAY DIFFRACTIONr_scbond_other4.8884.6092105
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5878.2073051
X-RAY DIFFRACTIONr_long_range_B_refined10.30342.764601
X-RAY DIFFRACTIONr_long_range_B_other10.23540.84566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 116 -
Rwork0.221 2209 -
obs--99.79 %

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