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- PDB-4wek: Crystal structure of Pseudomonas aeruginosa PBP3 with a R4 substi... -

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Basic information

Entry
Database: PDB / ID: 4wek
TitleCrystal structure of Pseudomonas aeruginosa PBP3 with a R4 substituted vinyl monocarbam
ComponentsPenicillin-binding protein 3
KeywordsPenicillin-binding protein/inhibitor / inhibitor / siderophore-conjugated monocarbams / Pseudomonas aeruginosa / penicillin-binding protein 3 / Penicillin-binding protein-inhibitor complex
Function / homology
Function and homology information


penicillin binding / carboxypeptidase activity / membrane
Similarity search - Function
Beta-Lactamase - #330 / 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 ...Beta-Lactamase - #330 / 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-3LC / Penicillin-binding protein 3 / :
Similarity search - Component
Biological speciesPseudomonas aeruginosa ATCC 14886 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsFerguson, A.D.
CitationJournal: Acs Med.Chem.Lett. / Year: 2015
Title: SAR and Structural Analysis of Siderophore-Conjugated Monocarbam Inhibitors of Pseudomonas aeruginosa PBP3.
Authors: Murphy-Benenato, K.E. / Dangel, B. / Davis, H.E. / Durand-Reville, T.F. / Ferguson, A.D. / Gao, N. / Jahic, H. / Mueller, J.P. / Manyak, E.L. / Quiroga, O. / Rooney, M. / Sha, L. / ...Authors: Murphy-Benenato, K.E. / Dangel, B. / Davis, H.E. / Durand-Reville, T.F. / Ferguson, A.D. / Gao, N. / Jahic, H. / Mueller, J.P. / Manyak, E.L. / Quiroga, O. / Rooney, M. / Sha, L. / Sylvester, M. / Wu, F. / Zambrowski, M. / Zhao, S.X.
History
DepositionSep 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1342
Polymers58,3451
Non-polymers7891
Water5,549308
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22650 Å2
Unit cell
Length a, b, c (Å)68.924, 83.232, 89.896
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 Penicillin-binding protein 3


Mass: 58345.453 Da / Num. of mol.: 1 / Mutation: A9S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa ATCC 14886 (bacteria)
Gene: ftsI, PABE171_4609 / Production host: Escherichia coli (E. coli) / References: UniProt: K1C6A4, UniProt: A0A0M3KKZ4*PLUS
#2: Chemical ChemComp-3LC / (3S,4S,7Z)-7-(2-amino-1,3-thiazol-4-yl)-3-ethenyl-4-formyl-1-[({3-(5-hydroxy-4-oxo-3,4-dihydropyridin-2-yl)-4-[3-(methylsulfonyl)propyl]-5-oxo-4,5-dihydro-1H-1,2,4-triazol-1-yl}sulfonyl)amino]-10,10-dimethyl-1,6-dioxo-9-oxa-2,5,8-triazaundec-7-en-11-oic acid


Mass: 788.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H32N10O13S3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 4000, 0.2M MgCl2, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.739→89.896 Å / Num. obs: 54364 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 28.48 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.3
Reflection shellResolution: 1.73→1.74 Å / Redundancy: 8 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
MOLREPphasing
Cootmodel building
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PBO

3pbo


Resolution: 1.74→45.71 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.111 / SU Rfree Blow DPI: 0.101 / SU Rfree Cruickshank DPI: 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2755 5.07 %RANDOM
Rwork0.186 ---
obs0.187 54299 99.3 %-
Displacement parametersBiso mean: 35.03 Å2
Baniso -1Baniso -2Baniso -3
1--6.8999 Å20 Å20 Å2
2---0.6151 Å20 Å2
3---7.5149 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 1.74→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 52 308 4180
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013962HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.035384HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1384SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes598HARMONIC5
X-RAY DIFFRACTIONt_it3962HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion17.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion509SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4922SEMIHARMONIC4
LS refinement shellResolution: 1.73→1.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2187 181 4.9 %
Rwork0.213 3514 -
all0.2133 3695 -
obs--99.34 %
Refinement TLS params.Method: refined / Origin x: 5.5827 Å / Origin y: 19.875 Å / Origin z: -1.4889 Å
111213212223313233
T-0.0888 Å2-0.0129 Å20.0129 Å2--0.0628 Å20.0137 Å2---0.0737 Å2
L0 °2-0.1549 °2-0.1849 °2-0.3738 °20.4973 °2--1.3689 °2
S0.0141 Å °0.0355 Å °0.0236 Å °-0.0627 Å °0.0595 Å °-0.0121 Å °-0.1182 Å °0.0621 Å °-0.0736 Å °
Refinement TLS groupSelection details: { A|* }

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