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- PDB-7kiw: Crystal structure of Pseudomonas aeruginosa PBP3 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7kiw
TitleCrystal structure of Pseudomonas aeruginosa PBP3 in complex with zidebactam
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE/Inhibitor/Antibiotic / Inhibitor / cell wall / antibiotic resistance / HYDROLASE / HYDROLASE-Inhibitor-Antibiotic complex
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane
Similarity search - Function
Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-C8V / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
Authorsvan den Akker, F. / Kumar, V.
CitationJournal: Mbio / Year: 2021
Title: Structural Characterization of Diazabicyclooctane beta-Lactam "Enhancers" in Complex with Penicillin-Binding Proteins PBP2 and PBP3 of Pseudomonas aeruginosa.
Authors: Rajavel, M. / Kumar, V. / Nguyen, H. / Wyatt, J. / Marshall, S.H. / Papp-Wallace, K.M. / Deshpande, P. / Bhavsar, S. / Yeole, R. / Bhagwat, S. / Patel, M. / Bonomo, R.A. / van den Akker, F.
History
DepositionOct 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: 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
Revision 1.3Oct 9, 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: Peptidoglycan D,D-transpeptidase FtsI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3262
Polymers62,9331
Non-polymers3931
Water1,29772
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)68.372, 80.025, 88.115
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 Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein 3 / PBP-3


Mass: 62933.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: ftsI, pbpB, PA4418 / Production host: Escherichia coli (E. coli)
References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-C8V / (2S,5R)-1-formyl-N'-[(3R)-piperidine-3-carbonyl]-5-[(sulfooxy)amino]piperidine-2-carbohydrazide / OPEN FORM - Zidebactam


Mass: 393.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H23N5O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 1.92 Å3/Da / Density % sol: 35.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% polyethylene glycol 4000, 0.2 M MgCl2, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.49→25 Å / Num. obs: 17225 / % possible obs: 99.9 % / Redundancy: 12 % / CC1/2: 0.997 / Rmerge(I) obs: 0.182 / Net I/σ(I): 22.3
Reflection shellResolution: 2.49→2.56 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.21 / Num. unique obs: 1711 / CC1/2: 0.942 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PBQ

3pbq


Resolution: 2.49→24.94 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.874 / SU B: 10.423 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.729 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2719 836 4.9 %RANDOM
Rwork0.1996 ---
obs0.2033 16353 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.18 Å2 / Biso mean: 46.553 Å2 / Biso min: 22.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.49→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3539 0 26 72 3637
Biso mean--74.82 42.08 -
Num. residues----466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133645
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173467
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.6534949
X-RAY DIFFRACTIONr_angle_other_deg1.1771.5868016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8455464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.69521.123187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53215590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6061532
X-RAY DIFFRACTIONr_chiral_restr0.0540.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024101
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02759
LS refinement shellResolution: 2.494→2.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 44 -
Rwork0.252 1026 -
all-1070 -
obs--84.65 %

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