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- PDB-5hfo: CRYSTAL STRUCTURE OF OXA-232 BETA-LACTAMASE -

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Basic information

Entry
Database: PDB / ID: 5hfo
TitleCRYSTAL STRUCTURE OF OXA-232 BETA-LACTAMASE
ComponentsBeta-lactamase
KeywordsHYDROLASE / CLASS D BETA-LACTAMASE OXA-232 / ANTIBIOTIC / DIMER
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsRetailleau, P. / Oueslati, S. / Cisse, C. / Nordmann, P. / Naas, T. / Iorga, B.
Funding support France, 1items
OrganizationGrant numberCountry
Laboratory of ExcellenceANR-10-LABX-33 France
CitationJournal: Antimicrob.Agents Chemother. / Year: 2020
Title: Role of Arginine 214 in the Substrate Specificity of OXA-48.
Authors: Oueslati, S. / Retailleau, P. / Marchini, L. / Berthault, C. / Dortet, L. / Bonnin, R.A. / Iorga, B.I. / Naas, T.
History
DepositionJan 7, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,15115
Polymers56,9822
Non-polymers1,16813
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-93 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.080, 144.080, 53.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Beta-lactamase / OXA-232


Mass: 28491.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaOXA-232 / Production host: Escherichia coli (E. coli) / References: UniProt: M4JTK1, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH 8.5, 30 %(W/V) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54187 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 3, 2013 / Details: VARIMAXHF MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.21→17.2 Å / Num. obs: 30557 / % possible obs: 97.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 13.8
Reflection shellResolution: 2.21→2.36 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 4.1 / % possible all: 90.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER-TNTBUSTER 2.10.1refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2.21→17.2 Å / Cor.coef. Fo:Fc: 0.9319 / Cor.coef. Fo:Fc free: 0.9191 / SU R Cruickshank DPI: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.256 / SU Rfree Blow DPI: 0.184 / SU Rfree Cruickshank DPI: 0.18
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 1534 5.05 %RANDOM
Rwork0.1719 ---
obs0.1738 30389 95.73 %-
Displacement parametersBiso max: 127.92 Å2 / Biso mean: 34.72 Å2 / Biso min: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1--5.9152 Å20 Å20 Å2
2---5.9152 Å20 Å2
3---11.8303 Å2
Refine analyzeLuzzati coordinate error obs: 0.248 Å
Refinement stepCycle: final / Resolution: 2.21→17.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3992 0 66 471 4529
Biso mean--48.9 42.85 -
Num. residues----489
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1456SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes123HARMONIC2
X-RAY DIFFRACTIONt_gen_planes588HARMONIC5
X-RAY DIFFRACTIONt_it4170HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion519SEMIHARMONIC5
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_contact4852SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4170HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5645HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion17.15
LS refinement shellResolution: 2.21→2.29 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.404 102 4.27 %
Rwork0.3432 2284 -
all0.3457 2386 -
obs--95.73 %
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)
11.8744-0.0729-0.081.2060.02950.66230.0495-0.02370.17980.028-0.0330.1139-0.0463-0.0369-0.0165-0.16540.01690.0579-0.18820.05790.247983.169523.93240.5227
21.5556-0.1432-0.30432.1337-0.29130.72940.06860.123-0.1035-0.1638-0.071-0.25870.0160.06010.0024-0.20480.01430.0243-0.20110.03610.2496100.5086-3.323-2.381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A24 - 266
2X-RAY DIFFRACTION2{ B|* }B23 - 268

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