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- PDB-6b22: Crystal structure OXA-24 beta-lactamase complexed with WCK 4234 b... -

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Basic information

Entry
Database: PDB / ID: 6b22
TitleCrystal structure OXA-24 beta-lactamase complexed with WCK 4234 by co-crystallization
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE Inhibitor / Inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex
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-C8Y / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
Authorsvan den Akker, F. / Nguyen, N.Q.
Funding support United States, 1items
OrganizationGrant numberCountry
Wockhardt United States
CitationJournal: J. Med. Chem. / Year: 2018
Title: Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using beta-Lactamase Inhibitors and beta-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, ...Title: Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using beta-Lactamase Inhibitors and beta-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, Zidebactam (WCK 5107), and WCK 4234.
Authors: Papp-Wallace, K.M. / Nguyen, N.Q. / Jacobs, M.R. / Bethel, C.R. / Barnes, M.D. / Kumar, V. / Bajaksouzian, S. / Rudin, S.D. / Rather, P.N. / Bhavsar, S. / Ravikumar, T. / Deshpande, P.K. / ...Authors: Papp-Wallace, K.M. / Nguyen, N.Q. / Jacobs, M.R. / Bethel, C.R. / Barnes, M.D. / Kumar, V. / Bajaksouzian, S. / Rudin, S.D. / Rather, P.N. / Bhavsar, S. / Ravikumar, T. / Deshpande, P.K. / Patil, V. / Yeole, R. / Bhagwat, S.S. / Patel, M.V. / van den Akker, F. / Bonomo, R.A.
History
DepositionSep 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8644
Polymers27,5441
Non-polymers3203
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.539, 102.539, 84.312
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Beta-lactamase / Beta-lactamase OXA-33 / Betalactamase OXA24 / Carbapenem-hydrolyzing beta-lactamase OXA-40 / ...Beta-lactamase OXA-33 / Betalactamase OXA24 / Carbapenem-hydrolyzing beta-lactamase OXA-40 / Carbapenem-hydrolyzing oxacillinase / Carbapenem-hydrolyzing oxacillinase OXA-40 / Carbapenemase OXA-24 / Class D beta-lactamase OXA-40 / OXA24 B-lactamase / Oxa40


Mass: 27543.658 Da / Num. of mol.: 1 / Fragment: UNP residues 32-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40
Production host: Escherichia coli (E. coli) / References: UniProt: Q8RLA6
#2: Chemical ChemComp-C8Y / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carbonitrile / open form - WCK 4234


Mass: 249.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 4.02 Å3/Da / Density % sol: 69.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Calcium acetate, 0.2M Sodium cacodylate pH 6.5, and 18% PEG 8000. Inhibitor:protein molar ratio 1:50.
Temp details: RT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.93→38.99 Å / Num. obs: 34171 / % possible obs: 99.3 % / Redundancy: 5.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.055 / Rrim(I) all: 0.138 / Net I/σ(I): 11.9 / Num. measured all: 198969 / Scaling rejects: 1348
Reflection shellResolution: 1.93→1.97 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.151 / Num. unique obs: 2247 / CC1/2: 0.656 / Rpim(I) all: 0.508 / Rrim(I) all: 1.261 / % possible all: 98.1

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→38 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.973 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.101
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1660 4.9 %RANDOM
Rwork0.1775 ---
obs0.1785 32457 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.64 Å2 / Biso mean: 24.027 Å2 / Biso min: 7.08 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.93→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 18 231 2185
Biso mean--39.88 35.36 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022005
X-RAY DIFFRACTIONr_bond_other_d0.0020.021962
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.962704
X-RAY DIFFRACTIONr_angle_other_deg0.9713.0024527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3675247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.61725.34188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43215380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.264158
X-RAY DIFFRACTIONr_chiral_restr0.2080.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022231
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02445
LS refinement shellResolution: 1.928→1.978 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 116 -
Rwork0.32 2326 -
all-2442 -
obs--97.56 %

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