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- PDB-4x55: Structure of the class D Beta-Lactamase OXA-225 K82D in Acyl-Enzy... -

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Basic information

Entry
Database: PDB / ID: 4x55
TitleStructure of the class D Beta-Lactamase OXA-225 K82D in Acyl-Enzyme Complex with Ceftazidime
ComponentsBeta-lactamase OXA-225
KeywordsHYDROLASE / Carbapenemase / Antibiotic
Function / homology
Function and homology information


penicillin binding / cell wall organization / beta-lactamase / plasma membrane
Similarity search - Function
: / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CTJ / beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.941 Å
AuthorsClasman, J.R. / June, C.M. / Powers, R.A. / Leonard, D.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R15AI082416-02 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R15AI094489 United States
CitationJournal: Biochemistry / Year: 2015
Title: Structural Basis of Activity against Aztreonam and Extended Spectrum Cephalosporins for Two Carbapenem-Hydrolyzing Class D beta-Lactamases from Acinetobacter baumannii.
Authors: Mitchell, J.M. / Clasman, J.R. / June, C.M. / Kaitany, K.C. / LaFleur, J.R. / Taracila, M.A. / Klinger, N.V. / Bonomo, R.A. / Wymore, T. / Szarecka, A. / Powers, R.A. / Leonard, D.A.
History
DepositionDec 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Apr 1, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase OXA-225
B: Beta-lactamase OXA-225
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6214
Polymers57,5222
Non-polymers1,0992
Water3,459192
1
A: Beta-lactamase OXA-225
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3112
Polymers28,7611
Non-polymers5501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase OXA-225
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3112
Polymers28,7611
Non-polymers5501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.779, 143.862, 44.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Beta-lactamase OXA-225 / OXA-23 class D beta-lactamase


Mass: 28761.072 Da / Num. of mol.: 2 / Mutation: K82D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaOXA-225, oxa23 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: G5DE28
#2: Chemical ChemComp-CTJ / 1-({(2R)-2-[(1R)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}-2-oxoethyl]-4-carboxy-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyridinium


Mass: 549.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25N6O7S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 100 mM NaH2PO4, 100 mM citric acid, 200 mM NaCl, 20% PEG 8000, pH 4.2
PH range: 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.941→143.9 Å / Num. obs: 47536 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.2
Reflection shellResolution: 1.941→1.948 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4K0X

4k0x


Resolution: 1.941→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.18 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26188 2403 5.1 %RANDOM
Rwork0.20917 ---
obs0.21181 45071 99.92 %-
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: 43.554 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å2-0 Å2-0 Å2
2--3.94 Å20 Å2
3----2.85 Å2
Refinement stepCycle: LAST / Resolution: 1.941→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3674 0 74 192 3940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193819
X-RAY DIFFRACTIONr_bond_other_d0.0010.023621
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.9745184
X-RAY DIFFRACTIONr_angle_other_deg0.74638269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.915470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71225.774168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93315643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.5971513
X-RAY DIFFRACTIONr_chiral_restr0.0960.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.024383
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02872
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.941→1.991 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 182 -
Rwork0.367 3214 -
obs--99.85 %

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