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- PDB-8sdr: Crystal structure of PDC-3 beta-lactamase in complex with the bor... -

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Basic information

Entry
Database: PDB / ID: 8sdr
TitleCrystal structure of PDC-3 beta-lactamase in complex with the boronic acid inhibitor LP-06
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Pseudomonas-derived Cephalosporinase / antibiotic resistance / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-CB4 / IMIDAZOLE / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsKumar, V. / van den Akker, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI063517 United States
CitationJournal: Antimicrob.Agents Chemother. / Year: 2023
Title: Natural protein engineering in the Omega-loop: the role of Y221 in ceftazidime and ceftolozane resistance in Pseudomonas -derived cephalosporinase.
Authors: Mack, A.R. / Kumar, V. / Taracila, M.A. / Mojica, M.F. / O'Shea, M. / Schinabeck, W. / Silver, G. / Hujer, A.M. / Papp-Wallace, K.M. / Chen, S. / Haider, S. / Caselli, E. / Prati, F. / van ...Authors: Mack, A.R. / Kumar, V. / Taracila, M.A. / Mojica, M.F. / O'Shea, M. / Schinabeck, W. / Silver, G. / Hujer, A.M. / Papp-Wallace, K.M. / Chen, S. / Haider, S. / Caselli, E. / Prati, F. / van den Akker, F. / Bonomo, R.A.
History
DepositionApr 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)43,8183
Polymers43,4191
Non-polymers3992
Water10,683593
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.828, 71.667, 106.729
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase


Mass: 43419.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ampC / Production host: Escherichia coli (E. coli) / References: UniProt: Q4H482, beta-lactamase
#2: Chemical ChemComp-CB4 / PINACOL[[2-AMINO-ALPHA-(1-CARBOXY-1-METHYLETHOXYIMINO)-4-THIAZOLEACETYL]AMINO]METHANEBORONATE


Mass: 330.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15BN4O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop
Details: 100 mM Imidazole pH 7.0, 2-8% isopropyl alcohol (IPA), and 16-34% PEG 3350. Protein was in 10 mM HEPES pH 7.5, 150 mM NaCl and 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.35→28 Å / Num. obs: 76325 / % possible obs: 99.7 % / Redundancy: 12.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.134 / Net I/σ(I): 14.8
Reflection shellResolution: 1.35→1.38 Å / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 3 / Num. unique obs: 5339 / CC1/2: 0.896 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→28 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.419 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1615 3919 5.1 %RANDOM
Rwork0.1292 ---
obs0.1309 72326 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.27 Å2 / Biso mean: 11.046 Å2 / Biso min: 3.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 1.35→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 27 593 3401
Biso mean--18.3 27.99 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133013
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172867
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.6544122
X-RAY DIFFRACTIONr_angle_other_deg1.4931.5796588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.60520.571175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89415482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1491529
X-RAY DIFFRACTIONr_chiral_restr0.0870.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023535
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02747
X-RAY DIFFRACTIONr_rigid_bond_restr1.28535880
LS refinement shellResolution: 1.35→1.384 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.291 271 -
Rwork0.279 5065 -
obs--96.09 %

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