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- PDB-6i1e: Crystal structure of Pseudomonas aeruginosa Penicillin-Binding Pr... -

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Basic information

Entry
Database: PDB / ID: 6i1e
TitleCrystal structure of Pseudomonas aeruginosa Penicillin-Binding Protein 3 in complex with amoxicillin
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsPEPTIDE BINDING PROTEIN / penicillin-binding protein / peptidoglycan / Transpeptidase
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
Beta-Lactamase - #330 / 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 / Beta-lactamase ...Beta-Lactamase - #330 / 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 / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AXL / Peptidoglycan D,D-transpeptidase FtsI / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsBellini, D. / Dowson, C.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)grant.MR/P007503/1 United Kingdom
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam ...Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam Target-Mediated Resistance.
Authors: Bellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G.
History
DepositionOct 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan D,D-transpeptidase FtsI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3942
Polymers58,0271
Non-polymers3671
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-4 kcal/mol
Surface area23580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.440, 82.780, 89.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 58027.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: pbpB, ftsI, ftsI_1, ftsI_2, AM489_25055, AO964_07895, AXW85_18330, C8257_27080, CAZ10_21230, CGU42_01090, CW299_32685, DI492_11155, NCTC12449_03360, PAERUG_E15_London_28_01_14_00534, RW109_RW109_05757
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q51504, UniProt: G3XD46*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-AXL / 2-{1-[2-AMINO-2-(4-HYDROXY-PHENYL)-ACETYLAMINO]-2-OXO-ETHYL}-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID / AMOXICILLIN, bound form


Mass: 367.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 25% (w/v) polyethylene glycol 3,350, 0.1M Bis-Tris propane pH 7.8 and 1% (w/v) protamine sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.64→60.75 Å / Num. obs: 62985 / % possible obs: 100 % / Redundancy: 9.8 % / Rrim(I) all: 0.094 / Net I/σ(I): 13.2
Reflection shellResolution: 1.64→1.67 Å

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
xia2data reduction
XSCALEdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HZR

6hzr


Resolution: 1.64→60.75 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.387 / SU ML: 0.08 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 3096 4.9 %RANDOM
Rwork0.21851 ---
obs0.21943 59815 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.556 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å2-0 Å20 Å2
2--0.2 Å20 Å2
3----1.72 Å2
Refinement stepCycle: 1 / Resolution: 1.64→60.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 0 168 4120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194031
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.9755472
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3525514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14923.059170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84315665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7151538
X-RAY DIFFRACTIONr_chiral_restr0.0750.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213063
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 199 -
Rwork0.361 4162 -
obs--99.95 %

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