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- PDB-4oom: Crystal structure of PBP3 in complex with BAL30072 ((2Z)-2-(2-ami... -

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Basic information

Entry
Database: PDB / ID: 4oom
TitleCrystal structure of PBP3 in complex with BAL30072 ((2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(1,5-dihydroxy-4-oxo-1,4-dihydropyridin-2-yl)methoxy]imino}-N-{(2S)-1-hydroxy-3-methyl-3-[(sulfooxy)amino]butan-2-yl}ethanamide)
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-2U3 / :
Function and homology information
Biological speciesPseudomonas aeruginosa PA1R (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Nov 27, 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: Cell division protein FtsI [Peptidoglycan synthetase]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8522
Polymers58,3291
Non-polymers5231
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.660, 82.820, 88.310
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: PBP3
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-2U3 / (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(1,5-dihydroxy-4-oxo-1,4-dihydropyridin-2-yl)methoxy]imino}-N-{(2S)-1-hydroxy-3-methyl-3-[(sulfooxy)amino]butan-2-yl}ethanamide


Mass: 522.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22N6O10S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.12 Å3/Da / Density % sol: 42.01 %
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→30 Å / Num. all: 148320 / Num. obs: 32905 / % possible obs: 95.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 29.82 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 81.6

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Processing

Software
NameClassification
HKL-2000data collection
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.52 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9393 / SU R Cruickshank DPI: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1655 5.05 %RANDOM
Rwork0.1866 ---
obs0.1886 32801 95.89 %-
all-32905 --
Displacement parametersBiso mean: 41.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.3131 Å20 Å20 Å2
2---0.962 Å20 Å2
3---2.2751 Å2
Refine analyzeLuzzati coordinate error obs: 0.262 Å
Refinement stepCycle: LAST / Resolution: 2→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3788 0 34 259 4081
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093902HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.085296HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1353SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes582HARMONIC5
X-RAY DIFFRACTIONt_it3902HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion17.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion502SEMIHARMONIC5
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_contact4705SEMIHARMONIC4
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2598 119 4.7 %
Rwork0.2313 2412 -
all0.2326 2531 -
obs--95.89 %
Refinement TLS params.Method: refined / Origin x: 5.1642 Å / Origin y: -19.7469 Å / Origin z: -1.7765 Å
111213212223313233
T-0.0892 Å20.006 Å20.0036 Å2--0.033 Å20.0184 Å2---0.071 Å2
L0.2817 °20.0609 °20.1049 °2-0.3494 °20.3859 °2--1.5555 °2
S-0.0177 Å °0.0979 Å °0.0783 Å °-0.062 Å °0.0007 Å °0.0216 Å °-0.0562 Å °0.098 Å °0.017 Å °
Refinement TLS groupSelection details: { A|* }

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