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- PDB-4wz5: Crystal structure of P. aeruginosa OXA10 -

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Basic information

Entry
Database: PDB / ID: 4wz5
TitleCrystal structure of P. aeruginosa OXA10
Components(Beta-lactamase OXA- ...) x 2
Keywordshydrolase/hydrolase inhibitor / beta lactamase / inhibtor / hydrolase-hydrolase inhibitor complex
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3VU / CARBON DIOXIDE / Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFerguson, A.D.
CitationJournal: Acs Infect Dis. / Year: 2015
Title: 4,5-Disubstituted 6-Aryloxy-1,3-dihydrobenzo[c][1,2]oxaboroles Are Broad-Spectrum Serine beta-Lactamase Inhibitors.
Authors: McKinney, D.C. / Zhou, F. / Eyermann, C.J. / Ferguson, A.D. / Prince, D.B. / Breen, J. / Giacobbe, R.A. / Lahiri, S. / Verheijen, J.C.
History
DepositionNov 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
C: Beta-lactamase OXA-10
D: Beta-lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,94321
Polymers110,9364
Non-polymers2,00717
Water9,062503
1
A: Beta-lactamase OXA-10
C: Beta-lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,42410
Polymers55,4682
Non-polymers9568
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-90 kcal/mol
Surface area20260 Å2
MethodPISA
2
B: Beta-lactamase OXA-10
D: Beta-lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,52011
Polymers55,4682
Non-polymers1,0529
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-106 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.740, 82.350, 102.380
Angle α, β, γ (deg.)90.00, 94.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Beta-lactamase OXA- ... , 2 types, 4 molecules ABCD

#1: Protein Beta-lactamase OXA-10 / Beta-lactamase PSE-2


Mass: 27755.541 Da / Num. of mol.: 2 / Mutation: K53KCX
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla, oxa10, pse2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14489, beta-lactamase
#2: Protein Beta-lactamase OXA-10 / Beta-lactamase PSE-2


Mass: 27712.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla, oxa10, pse2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14489, beta-lactamase

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Non-polymers , 4 types, 520 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-3VU / {(3R)-6-[(3-amino-1,2,4-thiadiazol-5-yl)oxy]-1-hydroxy-4,5-dimethyl-1,3-dihydro-2,1-benzoxaborol-3-yl}acetic acid


Mass: 335.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H14BN3O5S
#5: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→47 Å / Num. obs: 139523 / % possible obs: 97.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.78 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.1
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.3 / % possible all: 93.5

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→23.43 Å / Cor.coef. Fo:Fc: 0.9539 / Cor.coef. Fo:Fc free: 0.9431 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.086 / SU Rfree Blow DPI: 0.082 / SU Rfree Cruickshank DPI: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.208 6957 5.01 %RANDOM
Rwork0.1899 ---
obs0.1908 138980 97.03 %-
Displacement parametersBiso mean: 24.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.2382 Å20 Å21.2793 Å2
2---0.2293 Å20 Å2
3---0.4675 Å2
Refine analyzeLuzzati coordinate error obs: 0.246 Å
Refinement stepCycle: 1 / Resolution: 1.6→23.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7736 0 117 503 8356
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018039HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0110885HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2803SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes215HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1168HARMONIC5
X-RAY DIFFRACTIONt_it8039HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion16.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1023SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9688SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3214 519 5.21 %
Rwork0.2984 9451 -
all0.2996 9970 -
obs--97.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1727-0.11290.58230.5705-0.12111.295-0.02770.0144-0.02130.00390.0105-0.0986-0.13910.13210.0172-0.0435-0.0515-0.0075-0.0232-0.0217-0.038718.9228-3.549941.5633
21.404-0.4549-0.07440.8817-0.19840.61720.0192-0.095-0.1044-0.10710.07190.17780.0989-0.0933-0.0912-0.0642-0.048-0.0463-0.0220.0475-0.0161-21.11133.4251-13.1155
31.30120.0257-0.25640.6380.08230.8085-0.027-0.120.09940.02020.0530.0162-0.08050.0019-0.0260.01280.0155-0.0207-0.062-0.0112-0.0585-9.20919.414952.3332
41.253-0.06610.22870.654-0.1070.8113-0.0015-0.1016-0.0374-0.01490.05750.0128-0.00240.0081-0.056-0.04360.0005-0.0017-0.01610.0063-0.03125.106-8.93352.1455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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