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- PDB-2hp6: Crystal structure of the OXA-10 W154A mutant at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 2hp6
TitleCrystal structure of the OXA-10 W154A mutant at pH 7.5
ComponentsBeta-lactamase PSE-2
KeywordsHYDROLASE / class D beta-lactamase / lysine carboxylation
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKerff, F. / Falzone, C. / Herman, R. / Sauvage, E. / Charlier, P.
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
DepositionJul 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)55,6757
Polymers55,1952
Non-polymers4805
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-67 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.600, 96.720, 125.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer, composed from the two monomers A and B present in the asymmetric unit.

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Components

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


Mass: 27597.408 Da / Num. of mol.: 2 / Mutation: W154A, N-terminal Met added
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pse2, oxa10 / Plasmid: pET22BKanR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Hotstar / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M Ammonium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 21, 2005
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→19.4 Å / Num. all: 30362 / Num. obs: 30362 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 17.81 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 5.5 / Num. unique all: 4325 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1K4F

1k4f


Resolution: 2.2→19.4 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.956 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21133 1524 5 %RANDOM
Rwork0.16832 ---
obs0.17054 28742 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3860 0 25 322 4207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223960
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9535352
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.325489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27825.172174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1715713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7971516
X-RAY DIFFRACTIONr_chiral_restr0.0860.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022932
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21874
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22780
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6091.52522
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02323924
X-RAY DIFFRACTIONr_scbond_it1.71131683
X-RAY DIFFRACTIONr_scangle_it2.7394.51428
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 95 -
Rwork0.182 2056 -
obs-2151 97.42 %
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)
12.0339-0.8209-0.53622.40390.01972.5884-0.02050.1534-0.2211-0.1237-0.04190.20520.2779-0.15450.0624-0.0869-0.04960.0001-0.0627-0.0256-0.06864.92431.235555.0213
21.0823-0.1863-0.08741.277-0.01491.698-0.0498-0.0201-0.0060.08160.0049-0.0623-0.04680.02580.0449-0.1032-0.0035-0.0046-0.10930.004-0.102815.369814.38466.5745
31.42990.01630.21982.55970.30113.18840.0255-0.0468-0.08660.0166-0.01960.1811-0.0583-0.3647-0.0058-0.12710.0036-0.0107-0.02470.0239-0.07313.9481-8.052891.7065
41.9157-0.47-0.44081.2495-0.32572.83440.02870.0022-0.1567-0.1652-0.1219-0.15920.2980.13740.0932-0.06970.03730.0189-0.09180.0382-0.02521.5731-13.358683.0417
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA21 - 663 - 48
2X-RAY DIFFRACTION1AA193 - 264175 - 246
3X-RAY DIFFRACTION2AA67 - 19249 - 174
4X-RAY DIFFRACTION3BB21 - 663 - 48
5X-RAY DIFFRACTION3BB193 - 265175 - 247
6X-RAY DIFFRACTION4BB67 - 19249 - 174

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