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- PDB-6vje: Crystal structure of Pseudomonas aeruginosa penicillin-binding pr... -

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Basic information

Entry
Database: PDB / ID: 6vje
TitleCrystal structure of Pseudomonas aeruginosa penicillin-binding protein 3 (PBP3) complexed with ceftobiprole
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE / Antibiotic target / complex
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / 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-RB6 / Peptidoglycan D,D-transpeptidase FtsI / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
Authorsvan den Akker, F. / Kumar, V.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2020
Title: Structural Insights into Ceftobiprole Inhibition of Pseudomonas aeruginosa Penicillin-Binding Protein 3.
Authors: Kumar, V. / Tang, C. / Bethel, C.R. / Papp-Wallace, K.M. / Wyatt, J. / Desarbre, E. / Bonomo, R.A. / van den Akker, F.
History
DepositionJan 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 6, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3May 13, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)58,9374
Polymers58,3291
Non-polymers6073
Water4,360242
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)68.195, 83.739, 89.918
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: 58329.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: pbpB, ftsI, ftsI_2, ALP65_00912, CAZ10_21230, CGU42_01090, DZ934_06595, DZ962_00565, E4V10_06485, ECC04_026610, ERJ99_003095, FCG96_14995, FLI88_02250, IPC1481_11065, IPC1482_17070, IPC165_ ...Gene: pbpB, ftsI, ftsI_2, ALP65_00912, CAZ10_21230, CGU42_01090, DZ934_06595, DZ962_00565, E4V10_06485, ECC04_026610, ERJ99_003095, FCG96_14995, FLI88_02250, IPC1481_11065, IPC1482_17070, IPC165_24935, IPC170_23205, IPC669_10550, RW109_RW109_05757
Production host: Escherichia coli (E. coli)
References: UniProt: Q51504, UniProt: G3XD46*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-RB6 / (2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / BAL 9141, bound form / ceftobiprole, bound form


Mass: 536.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N8O6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 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: BL14-1 / Wavelength: 1.195 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.195 Å / Relative weight: 1
ReflectionResolution: 1.76→39.61 Å / Num. obs: 51816 / % possible obs: 99.8 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 25.2
Reflection shellResolution: 1.76→1.79 Å / Rmerge(I) obs: 0.984 / Num. unique obs: 2811 / % possible all: 96.6

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PBQ

3pbq


Resolution: 1.76→39.61 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.306 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.131
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 2592 5 %RANDOM
Rwork0.2048 ---
obs0.2072 49145 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 195.22 Å2 / Biso mean: 45 Å2 / Biso min: 17.94 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.76→39.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3832 0 38 242 4112
Biso mean--40.77 42.87 -
Num. residues----502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193981
X-RAY DIFFRACTIONr_bond_other_d0.0020.023895
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9745404
X-RAY DIFFRACTIONr_angle_other_deg0.9713.0038928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8375510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.81323.118170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03515661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4621538
X-RAY DIFFRACTIONr_chiral_restr0.070.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214536
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02906
LS refinement shellResolution: 1.76→1.804 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.368 193 -
Rwork0.32 3464 -
obs--96.98 %

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