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- PDB-5fdh: CRYSTAL STRUCTURE OF OXA-405 BETA-LACTAMASE -

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Basic information

Entry
Database: PDB / ID: 5fdh
TitleCRYSTAL STRUCTURE OF OXA-405 BETA-LACTAMASE
ComponentsBeta-lactamase
KeywordsHYDROLASE / CLASS D BETA-LACTAMASE OXA-405 / ANTIBIOTIC
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 speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsRetailleau, P. / Oueslati, S. / Marchini, L. / Dortet, L. / Naas, T. / Iorga, B.
Funding support France, 1items
OrganizationGrant numberCountry
Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT)ANR-10-LABX-33 France
CitationJournal: Microorganisms / Year: 2019
Title: Biochemical and Structural Characterization of OXA-405, an OXA-48 Variant with Extended-Spectrum beta-Lactamase Activity.
Authors: Oueslati, S. / Retailleau, P. / Marchini, L. / Dortet, L. / Bonnin, R.A. / Iorga, B.I. / Naas, T.
History
DepositionDec 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name / _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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,74716
Polymers58,4102
Non-polymers1,33714
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-144 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.400, 90.400, 172.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Beta-lactamase


Mass: 29205.012 Da / Num. of mol.: 2 / Fragment: UNP residues 23-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: blaOXA-405 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6P2I5, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium fluoride, 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 30, 2014
RadiationMonochromator: Varimax HF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.26→13.12 Å / Num. obs: 33544 / % possible obs: 98.2 % / Redundancy: 8.8 % / Biso Wilson estimate: 37.93 Å2 / Rsym value: 0.092 / Net I/σ(I): 18.9
Reflection shellResolution: 2.26→2.4 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.6 / % possible all: 90.3

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
MOSFLM1.0.7data reduction
MOLREP11.2.05phasing
XDS2014data reduction
XSCALE2014data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2P

4s2p


Resolution: 2.26→13.12 Å / Cor.coef. Fo:Fc: 0.9066 / Cor.coef. Fo:Fc free: 0.8915 / SU R Cruickshank DPI: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.238 / SU Rfree Blow DPI: 0.184 / SU Rfree Cruickshank DPI: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 1671 5 %RANDOM
Rwork0.1746 ---
obs0.1765 33404 97.97 %-
Displacement parametersBiso mean: 39.51 Å2
Baniso -1Baniso -2Baniso -3
1-9.3614 Å20 Å20 Å2
2--9.3614 Å20 Å2
3----18.7228 Å2
Refine analyzeLuzzati coordinate error obs: 0.275 Å
Refinement stepCycle: LAST / Resolution: 2.26→13.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 72 434 4458
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014137HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.15605HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1435SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes119HARMONIC2
X-RAY DIFFRACTIONt_gen_planes582HARMONIC5
X-RAY DIFFRACTIONt_it4137HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion17.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion511SEMIHARMONIC5
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_contact5036SEMIHARMONIC4
LS refinement shellResolution: 2.26→2.33 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2677 112 5 %
Rwork0.2116 2130 -
all0.2143 2242 -
obs--97.97 %
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)
12.11660.5555-0.11061.4269-0.20890.5891-0.14470.2559-0.126-0.18020.08280.05660.134-0.07960.06180.0054-0.09250.05670.0068-0.069-0.165924.678757.6772-6.5144
21.75890.4156-0.37241.88530.3571.06720.0097-0.16840.37680.0183-0.00980.0762-0.1120.00080.0001-0.054-0.05850.031-0.038-0.0943-0.108131.306584.41459.8346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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