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- PDB-4ool: Crystal structure of PBP3 in complex with compound 14 ((2E)-2-({[... -

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Basic information

Entry
Database: PDB / ID: 4ool
TitleCrystal structure of PBP3 in complex with compound 14 ((2E)-2-({[(2S)-2-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(1,5-dihydroxy-4-oxo-1,4-dihydropyridin-2-yl)methoxy]imino}acetyl]amino}-3-oxopropyl]oxy}imino)pentanedioic acid)
ComponentsCell division protein FtsI [Peptidoglycan synthetase]
Keywordstransferase/transferase inhibitor / PBP3 / transferase-transferase inhibitor complex
Function / homologyBeta-Lactamase - #330 / Beta-Lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / Chem-2U2 / :
Function and homology information
Biological speciesPseudomonas aeruginosa PA1R (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHan, S. / Caspers, N. / Knafels, J.D.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Siderophore receptor-mediated uptake of lactivicin analogues in gram-negative bacteria.
Authors: Starr, J. / Brown, M.F. / Aschenbrenner, L. / Caspers, N. / Che, Y. / Gerstenberger, B.S. / Huband, M. / Knafels, J.D. / Lemmon, M.M. / Li, C. / McCurdy, S.P. / McElroy, E. / Rauckhorst, M.R. ...Authors: Starr, J. / Brown, M.F. / Aschenbrenner, L. / Caspers, N. / Che, Y. / Gerstenberger, B.S. / Huband, M. / Knafels, J.D. / Lemmon, M.M. / Li, C. / McCurdy, S.P. / McElroy, E. / Rauckhorst, M.R. / Tomaras, A.P. / Young, J.A. / Zaniewski, R.P. / Shanmugasundaram, V. / Han, S.
History
DepositionFeb 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / 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 / _software.name / _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: Cell division protein FtsI [Peptidoglycan synthetase]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8702
Polymers58,3291
Non-polymers5401
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.280, 83.540, 89.250
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 Cell division protein FtsI [Peptidoglycan synthetase]


Mass: 58329.453 Da / Num. of mol.: 1 / Fragment: penicillin binding protein, unp residues 50-579
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PA1R (bacteria) / Gene: PA1R_gp2318 / Production host: Escherichia coli (E. coli)
References: UniProt: U6AVY0, peptidoglycan glycosyltransferase
#2: Chemical ChemComp-2U2 / (2E)-2-({[(2S)-2-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(1,5-dihydroxy-4-oxo-1,4-dihydropyridin-2-yl)methoxy]imino}acetyl]amino}-3-oxopropyl]oxy}imino)pentanedioic acid


Mass: 540.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N6O11S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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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: 43.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4K, 0.2M MgCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 18, 2012
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. all: 142397 / Num. obs: 23399 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 60.21 Å2 / Rmerge(I) obs: 0.045
Reflection shellResolution: 2.287→2.294 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.2 / % possible all: 77.4

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Processing

Software
NameClassification
autoPROCdata collection
BUSTERrefinement
autoPROCdata scaling
SCALAdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3PBN

3pbn


Resolution: 2.3→27.27 Å / Cor.coef. Fo:Fc: 0.9441 / Cor.coef. Fo:Fc free: 0.9198 / SU R Cruickshank DPI: 0.313 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 1198 5.15 %RANDOM
Rwork0.1861 ---
obs0.189 23258 98.64 %-
all-26575 --
Displacement parametersBiso mean: 70.86 Å2
Baniso -1Baniso -2Baniso -3
1--11.2197 Å20 Å20 Å2
2---2.2409 Å20 Å2
3---13.4606 Å2
Refine analyzeLuzzati coordinate error obs: 0.351 Å
Refinement stepCycle: LAST / Resolution: 2.3→27.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 37 107 3954
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013937HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.165345HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1368SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes591HARMONIC5
X-RAY DIFFRACTIONt_it3937HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion18.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion509SEMIHARMONIC5
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_contact4577SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.39 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2968 121 4.8 %
Rwork0.2242 2401 -
all0.2274 2522 -
obs--98.64 %
Refinement TLS params.Method: refined / Origin x: 28.9717 Å / Origin y: 20.8355 Å / Origin z: -1.1898 Å
111213212223313233
T-0.2269 Å2-0.018 Å20.006 Å2--0.0691 Å2-0.0214 Å2---0.1984 Å2
L0.2539 °2-0.7482 °21.0141 °2-1.0937 °2-1.4703 °2--3.6323 °2
S0.047 Å °0.1796 Å °-0.0448 Å °-0.1712 Å °0.0526 Å °-0.0581 Å °0.2995 Å °-0.1035 Å °-0.0997 Å °
Refinement TLS groupSelection details: { A|53 - A|561 }

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