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- PDB-4l0l: Crystal structure of P.aeruginosa PBP3 in complex with compound 4 -

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Basic information

Entry
Database: PDB / ID: 4l0l
TitleCrystal structure of P.aeruginosa PBP3 in complex with compound 4
ComponentsPenicillin-binding protein 3
KeywordsPenicillin Binding Protein/Antibiotic / Penicillin Binding Protein 3 / Penicillin Binding Protein-Antibiotic complex
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / 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-PFV / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsHan, S. / Marr, E.S.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Pyridone-conjugated monobactam antibiotics with gram-negative activity.
Authors: Brown, M.F. / Mitton-Fry, M.J. / Arcari, J.T. / Barham, R. / Casavant, J. / Gerstenberger, B.S. / Han, S. / Hardink, J.R. / Harris, T.M. / Hoang, T. / Huband, M.D. / Lall, M.S. / Lemmon, M.M. ...Authors: Brown, M.F. / Mitton-Fry, M.J. / Arcari, J.T. / Barham, R. / Casavant, J. / Gerstenberger, B.S. / Han, S. / Hardink, J.R. / Harris, T.M. / Hoang, T. / Huband, M.D. / Lall, M.S. / Lemmon, M.M. / Li, C. / Lin, J. / McCurdy, S.P. / McElroy, E. / McPherson, C. / Marr, E.S. / Mueller, J.P. / Mullins, L. / Nikitenko, A.A. / Noe, M.C. / Penzien, J. / Plummer, M.S. / Schuff, B.P. / Shanmugasundaram, V. / Starr, J.T. / Sun, J. / Tomaras, A. / Young, J.A. / Zaniewski, R.P.
History
DepositionMay 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)58,8262
Polymers58,1911
Non-polymers6351
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.725, 82.832, 88.689
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: 58191.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pbpB / Production host: Escherichia coli (E. coli) / References: UniProt: Q51504
#2: Chemical ChemComp-PFV / (6R,7S,10Z)-10-(2-amino-1,3-thiazol-4-yl)-1-(1,5-dihydroxy-4-oxo-1,4-dihydropyridin-2-yl)-7-formyl-13,13-dimethyl-3,9-dioxo-6-(sulfoamino)-12-oxa-2,4,8,11-tetraazatetradec-10-en-14-oic acid


Mass: 634.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N8O12S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.2M MgCl2, 0.1M Tris pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2010
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 29128 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.36 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMACrefinement
BUSTER2.9.2refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→22.27 Å / Cor.coef. Fo:Fc: 0.9336 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2754 1473 5.08 %RANDOM
Rwork0.2076 ---
obs0.2109 29005 --
Displacement parametersBiso mean: 34.85 Å2
Baniso -1Baniso -2Baniso -3
1--2.9878 Å20 Å20 Å2
2---1.5501 Å20 Å2
3---4.5379 Å2
Refine analyzeLuzzati coordinate error obs: 0.286 Å
Refinement stepCycle: LAST / Resolution: 2.1→22.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 42 256 4120
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093941HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.15353HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1348SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes100HARMONIC2
X-RAY DIFFRACTIONt_gen_planes582HARMONIC5
X-RAY DIFFRACTIONt_it3941HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion18.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion511SEMIHARMONIC5
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_contact4729SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.17 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2409 117 4.52 %
Rwork0.2248 2474 -
all0.2256 2591 -

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