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- PDB-2rl3: Crystal structure of the OXA-10 W154H mutant at pH 7 -

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Basic information

Entry
Database: PDB / ID: 2rl3
TitleCrystal structure of the OXA-10 W154H mutant at pH 7
ComponentsBeta-lactamase PSE-2
KeywordsHYDROLASE / OXA-10 / carboxylated lysine / class D beta-lactamase / Antibiotic resistance
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
Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVercheval, L. / Kerff, F. / Herman, R. / Sauvage, E. / Guiet, R. / Charlier, P. / Frere, J.-M. / Galleni, M.
CitationJournal: Biochemistry / Year: 2009
Title: Critical role of tryptophan 154 for the activity and stability of class D beta-lactamases.
Authors: Baurin, S. / Vercheval, L. / Bouillenne, F. / Falzone, C. / Brans, A. / Jacquamet, L. / Ferrer, J.L. / Sauvage, E. / Dehareng, D. / Frere, J.M. / Charlier, P. / Galleni, M. / Kerff, F.
History
DepositionOct 18, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase PSE-2
B: Beta-lactamase PSE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,51615
Polymers55,3292
Non-polymers1,18713
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-79 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.680, 97.060, 125.680
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 PSE-2 / Beta lactamase OXA-10


Mass: 27664.477 Da / Num. of mol.: 2 / Mutation: W154H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pse2, oxa10 / Plasmid: pET 22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsLYS A 70 AND KCX (LYSINE NZ-CARBOXYLIC ACID) A 70 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. IN ...LYS A 70 AND KCX (LYSINE NZ-CARBOXYLIC ACID) A 70 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. IN CHAIN A, THE STRUCTURE WAS MODELLED AS A MIXTURE OF CARBONATED AND UNCARBONATED FORM.

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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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.6M AS, 0.1M HEPES, PEG 30%, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.978872 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978872 Å / Relative weight: 1
ReflectionResolution: 1.9→48.68 Å / Num. obs: 47547 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 10.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.7 / Num. unique all: 6568 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K4F

1k4f


Resolution: 1.9→48.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.264 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.13 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21815 2400 5.1 %RANDOM
Rwork0.16863 ---
obs0.17109 45064 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2--0.33 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3899 0 71 353 4323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224070
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9615493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6815504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83425.196179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97715732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1241516
X-RAY DIFFRACTIONr_chiral_restr0.1090.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023001
X-RAY DIFFRACTIONr_nbd_refined0.2080.21910
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22809
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2740.218
X-RAY DIFFRACTIONr_mcbond_it2.51322554
X-RAY DIFFRACTIONr_mcangle_it3.37133988
X-RAY DIFFRACTIONr_scbond_it3.04421750
X-RAY DIFFRACTIONr_scangle_it4.29431500
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 161 -
Rwork0.254 3069 -
obs-3230 92.82 %
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)
112.0234-0.30737.28822.4132-2.86257.39550.09570.24190.5018-0.1257-0.3137-0.172-0.47990.30040.2180.1362-0.03980.03690.04830.0726-0.01718.904352.814246.3872
20.1569-0.0657-0.40761.1462-0.61352.2068-0.05370.05820.0159-0.0693-0.0281-0.0548-0.0791-0.05310.08170.0474-0.0111-0.02080.06830.00010.049112.995242.25255.6172
36.0276-3.6325-3.32372.21632.26514.3593-0.3571-0.12-0.00690.35650.15930.02320.23640.14140.19780.06550.01310.02180.0431-0.00780.061917.452229.641277.3599
42.08910.84911.23310.79331.03082.1831-0.0825-0.027-0.09450.0120.0617-0.0144-0.0163-0.07490.02080.07350.01640.01380.05220.00150.037210.724130.174369.6951
50.7192-0.0902-0.10061.38120.29581.2467-0.04760.03430.0335-0.00070.03850.0575-0.038-0.07550.00910.04220.0078-0.00790.074-0.00140.04365.713337.576560.6414
60.6264-1.2374-0.25544.94253.63074.01610.0839-0.11180.0799-0.37820.0668-0.2859-0.34880.1537-0.15070.0876-0.03950.01690.04100.078620.300644.402962.915
71.8082-1.6945-0.00253.1760.4221.4378-0.0439-0.10560.1154-0.01610.0544-0.1236-0.22970.1582-0.01050.0653-0.0421-0.01810.05510.00390.035420.758347.547357.7767
810.32828.0524-9.0511.7138-7.60567.98560.0657-0.6401-0.43980.4517-0.4536-0.7140.06750.73930.38790.0611-0.0254-0.06780.1721-0.0169-0.030724.482452.4784100.0148
91.06060.15830.59720.86890.57312.2542-0.004-0.0340.22260.0457-0.10290.0585-0.0446-0.02520.1070.0488-0.00370.02690.0184-0.01930.028110.824557.177191.2631
108.14510.67311.274727.80615.85418.6894-0.40720.07140.8045-2.1584-0.0751-0.0789-1.7580.09140.48230.48760.1517-0.08-0.04840.05730.23186.584371.926571.6365
113.3970.5141-1.6122.1916-0.64743.50990.21350.07490.3099-0.2252-0.23780.3269-0.4962-0.24870.02420.06850.0675-0.05980.0042-0.04870.06880.010664.008982.5748
126.583-0.02085.83450.13681.001812.783-0.7672-0.24481.1624-0.3109-0.4519-0.1826-2.048-0.19891.21910.43950.0931-0.12320.0386-0.13930.32471.230767.863193.3588
131.2589-0.29020.07380.98630.32781.75470.00280.0250.0323-0.0518-0.01640.0268-0.0455-0.00470.01360.0520.00950.00040.0437-0.02950.05039.829754.597286.0832
140.62570.40980.35745.35461.25242.1129-0.04480.05830.0624-0.08170.0457-0.0076-0.13670.2739-0.00090.016-0.0260.02060.1003-0.0270.027720.836857.068989.2374
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA19 - 321 - 14
2X-RAY DIFFRACTION2AA33 - 8315 - 65
3X-RAY DIFFRACTION3AA84 - 10466 - 86
4X-RAY DIFFRACTION4AA105 - 13387 - 115
5X-RAY DIFFRACTION5AA134 - 192116 - 174
6X-RAY DIFFRACTION6AA193 - 215175 - 197
7X-RAY DIFFRACTION7AA216 - 264198 - 246
8X-RAY DIFFRACTION8BB19 - 331 - 15
9X-RAY DIFFRACTION9BB34 - 8616 - 68
10X-RAY DIFFRACTION10BB87 - 10469 - 86
11X-RAY DIFFRACTION11BB105 - 13987 - 121
12X-RAY DIFFRACTION12BB140 - 158122 - 140
13X-RAY DIFFRACTION13BB159 - 215141 - 197
14X-RAY DIFFRACTION14BB216 - 264198 - 246

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