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

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Basic information

Entry
Database: PDB / ID: 4wej
TitleCrystal structure of Pseudomonas aeruginosa PBP3 with a R4 substituted allyl 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 / proteolysis / 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-3LB / Penicillin-binding protein 3 / :
Similarity search - Component
Biological speciesPseudomonas aeruginosa PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.045 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 / Structure summary
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_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords
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_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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 / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1322
Polymers58,3291
Non-polymers8031
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22110 Å2
Unit cell
Length a, b, c (Å)67.788, 83.047, 88.801
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: 58329.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Gene: CIA_00399 / Production host: Escherichia coli (E. coli) / References: UniProt: S0J4R2, UniProt: A0A0M3KKZ3*PLUS
#2: Chemical ChemComp-3LB / (3R,4S,7Z)-7-(2-amino-1,3-thiazol-4-yl)-4-formyl-1-[({3-[(5R)-5-hydroxy-4-oxo-4,5-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-3-(prop-2-en-1-yl)-9-oxa-2,5,8-triazaundec-7-en-11-oic acid


Mass: 802.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H34N10O13S3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
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: 2.045→88.081 Å / Num. obs: 32015 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 32.34 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 18
Reflection shellResolution: 2.045→2.051 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 3.8 / % possible all: 98.2

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Processing

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

3pbo


Resolution: 2.045→53.88 Å / Cor.coef. Fo:Fc: 0.9345 / Cor.coef. Fo:Fc free: 0.8921 / SU R Cruickshank DPI: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.195 / SU Rfree Blow DPI: 0.164 / SU Rfree Cruickshank DPI: 0.164
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 1627 5.09 %RANDOM
Rwork0.1839 ---
obs0.1859 31969 98.03 %-
Displacement parametersBiso mean: 40.19 Å2
Baniso -1Baniso -2Baniso -3
1--4.9852 Å20 Å20 Å2
2---0.066 Å20 Å2
3---5.0512 Å2
Refine analyzeLuzzati coordinate error obs: 0.233 Å
Refinement stepCycle: 1 / Resolution: 2.045→53.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3826 0 53 171 4050
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013957HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.045376HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1380SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes600HARMONIC5
X-RAY DIFFRACTIONt_it3957HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion17.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion508SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4687SEMIHARMONIC4
LS refinement shellResolution: 2.04→2.11 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.227 138 5.11 %
Rwork0.2009 2565 -
all0.2023 2703 -
obs--98.03 %
Refinement TLS params.Method: refined / Origin x: -5.7257 Å / Origin y: 21.3028 Å / Origin z: 1.7275 Å
111213212223313233
T-0.1031 Å20.0002 Å20.0052 Å2--0.0369 Å2-0.0126 Å2---0.0607 Å2
L0.1167 °2-0.0039 °20.1048 °2-0.5081 °2-0.5015 °2--1.3303 °2
S-0.0057 Å °-0.0825 Å °0.0448 Å °0.0687 Å °0.0074 Å °-0.0216 Å °-0.0868 Å °-0.0946 Å °-0.0018 Å °
Refinement TLS groupSelection details: { A|* }

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