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- PDB-4oon: Crystal structure of PBP1a in complex with compound 17 ((4Z,8S,11... -

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Basic information

Entry
Database: PDB / ID: 4oon
TitleCrystal structure of PBP1a in complex with compound 17 ((4Z,8S,11E,14S)-5-(2-amino-1,3-thiazol-4-yl)-14-(5,6-dihydroxy-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)-8-formyl-2-methyl-6-oxo-3,10-dioxa-4,7,11-triazatetradeca-4,11-diene-2,12,14-tricarboxylic acid)
ComponentsPenicillin-binding protein 1A
Keywordstransferase/transferase inhibitor / PBP1A / transferase-transferase inhibitor complex
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / plasma membrane
Similarity search - Function
Penicillin-binding protein, OB-like domain / Penicillin-binding protein OB-like domain / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / : / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Nucleic acid-binding proteins / Beta-lactamase ...Penicillin-binding protein, OB-like domain / Penicillin-binding protein OB-like domain / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / : / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Nucleic acid-binding proteins / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Lysozyme-like domain superfamily / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-2U4 / Penicillin-binding protein 1A
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 1.2Mar 6, 2024Group: 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 / 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: Penicillin-binding protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0442
Polymers88,3801
Non-polymers6651
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.770, 113.770, 123.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Penicillin-binding protein 1A / PBP-1a / PBP1a / Penicillin-insensitive transglycosylase / Peptidoglycan TGase / Penicillin- ...PBP-1a / PBP1a / Penicillin-insensitive transglycosylase / Peptidoglycan TGase / Penicillin-sensitive transpeptidase / DD-transpeptidase


Mass: 88379.742 Da / Num. of mol.: 1 / Fragment: PBP1A: unp residues 36-822
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: mrcA, ponA, PA5045 / Production host: Escherichia coli (E. coli)
References: UniProt: Q07806, Transferases; Glycosyltransferases; Pentosyltransferases, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-2U4 / (4Z,8S,11E,14S)-5-(2-amino-1,3-thiazol-4-yl)-14-(5,6-dihydroxy-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)-8-formyl-2-methyl-6-oxo-3,10-dioxa-4,7,11-triazatetradeca-4,11-diene-2,12,14-tricarboxylic acid


Mass: 664.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H24N6O14S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate pH 5.6, 1.2M ammonium phosphate, VAPOR DIFFUSION, HANGING DROP

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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: 3.2→100 Å / Num. all: 175377 / Num. obs: 13985 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 93.05 Å2
Reflection shellResolution: 3.199→3.21 Å / % possible all: 100

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Processing

Software
NameClassification
autoPROCdata collection
BUSTERrefinement
autoPROCdata scaling
SCALAdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→27.72 Å / Cor.coef. Fo:Fc: 0.9338 / Cor.coef. Fo:Fc free: 0.9034 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 693 4.99 %RANDOM
Rwork0.168 ---
obs0.1702 13898 100 %-
all-13985 --
Displacement parametersBiso mean: 82.04 Å2
Baniso -1Baniso -2Baniso -3
1-10.7362 Å20 Å20 Å2
2--10.7362 Å20 Å2
3----21.4724 Å2
Refine analyzeLuzzati coordinate error obs: 0.555 Å
Refinement stepCycle: LAST / Resolution: 3.2→27.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 46 2 3959
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014045HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.215481HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1396SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes596HARMONIC5
X-RAY DIFFRACTIONt_it4045HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion20.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion518SEMIHARMONIC5
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_contact4818SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.46 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2777 162 5.76 %
Rwork0.1902 2649 -
all0.1952 2811 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -27.8957 Å / Origin y: 25.2953 Å / Origin z: 1.187 Å
111213212223313233
T-0.093 Å2-0.0167 Å20.0989 Å2--0.0521 Å2-0.0155 Å2---0.1247 Å2
L0.7094 °2-0.1666 °20.0006 °2-2.1637 °20.611 °2--0.7179 °2
S-0.0499 Å °0.0005 Å °-0.0583 Å °-0.1534 Å °0.2304 Å °-0.1612 Å °-0.0356 Å °0.0176 Å °-0.1805 Å °
Refinement TLS groupSelection details: { A|* }

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