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- PDB-3fyz: OXA-24 beta-lactamase complex with SA4-17 inhibitor -

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Basic information

Entry
Database: PDB / ID: 3fyz
TitleOXA-24 beta-lactamase complex with SA4-17 inhibitor
ComponentsBeta-lactamase OXA-24
KeywordsHYDROLASE / B-LACTAMASES / ENZYME MECHANISM / CARBAPENEM / INHIBITORS
Function / homology
Function and homology information


penicillin binding / beta-lactamase activity
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-MXC / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRomero, A. / Santillana, E.
Citation
Journal: J.Am.Chem.Soc. / Year: 2010
Title: Design, synthesis, and crystal structures of 6-alkylidene-2'-substituted penicillanic acid sulfones as potent inhibitors of Acinetobacter baumannii OXA-24 carbapenemase.
Authors: Bou, G. / Santillana, E. / Sheri, A. / Beceiro, A. / Sampson, J.M. / Kalp, M. / Bethel, C.R. / Distler, A.M. / Drawz, S.M. / Pagadala, S.R. / van den Akker, F. / Bonomo, R.A. / Romero, A. / Buynak, J.D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Crystal structure of the carbapenemase OXA-24 reveals insights into the mechanism of carbapenem hydrolysis.
Authors: Santillana, E. / Beceiro, A. / Bou, G. / Romero, A.
History
DepositionJan 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase OXA-24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2073
Polymers27,5871
Non-polymers6212
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.760, 102.760, 83.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Beta-lactamase OXA-24 / Beta-lactamase OXA-33 / Oxa40 / Carbapenem-hydrolyzing beta-lactamase OXA-40 / Beta-lactamase


Mass: 27586.660 Da / Num. of mol.: 1 / Fragment: residues 32-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaOXA-33, bla-OXA-40, oxa-24, oxa40 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q8RLA6, beta-lactamase
#2: Chemical ChemComp-MXC / (2S,3R)-2-[(7-aminocarbonyl-2-methanoyl-indolizin-3-yl)amino]-4-aminocarbonyloxy-3-methyl-3-sulfino-butanoic acid


Mass: 426.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N4O8S
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3.98 Å3/Da / Density % sol: 69.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M SODIUM ACETATE, 28% PEG 2000 MME, 0.1M HEPES (PH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 19, 2008
RadiationMonochromator: SINGLE SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.1→72.7 Å / Num. all: 26542 / Num. obs: 26313 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 28.45 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 14.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3534 / % possible all: 93.9

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Processing

Software
NameClassification
DNAdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JC7

2jc7


Resolution: 2.1→54.72 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1271 -RANDOM
Rwork0.232 ---
obs0.232 26265 98.7 %-
all-26313 --
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.1→54.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 42 79 2060
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.38 206 -
Rwork0.373 --
obs-3861 93.5 %

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