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- PDB-7lc4: Crystal structure of Pseudomonas aeruginosa PBP3 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7lc4
TitleCrystal structure of Pseudomonas aeruginosa PBP3 in complex with gamma-lactam YU253911
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE/HYDROLASE Inhibitor / PBP3 / gamma-lactam / inhibitor complex / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane
Similarity search - Function
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/transpeptidase-like
Similarity search - Domain/homology
Chem-XVG / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
Authorsvan den Akker, F. / Kumar, V.
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: A gamma-lactam siderophore antibiotic effective against multidrug-resistant Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter spp.
Authors: Goldberg, J.A. / Kumar, V. / Spencer, E.J. / Hoyer, D. / Marshall, S.H. / Hujer, A.M. / Hujer, K.M. / Bethel, C.R. / Papp-Wallace, K.M. / Perez, F. / Jacobs, M.R. / van Duin, D. / ...Authors: Goldberg, J.A. / Kumar, V. / Spencer, E.J. / Hoyer, D. / Marshall, S.H. / Hujer, A.M. / Hujer, K.M. / Bethel, C.R. / Papp-Wallace, K.M. / Perez, F. / Jacobs, M.R. / van Duin, D. / Kreiswirth, B.N. / van den Akker, F. / Plummer, M.S. / Bonomo, R.A.
History
DepositionJan 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan D,D-transpeptidase FtsI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0532
Polymers58,3291
Non-polymers7231
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.765, 82.661, 88.799
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein 3 / PBP-3


Mass: 58329.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pbpB, ftsI, ftsI_2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q51504, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-XVG / 1-[(2S)-2-{[(2Z)-2-(2-amino-5-chloro-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}-3-oxopropyl]-4-{[2-(5,6-dihydroxy-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl]carbamoyl}-2,5-dihydro-1H-pyrazole-3-carboxylic acid


Mass: 723.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27ClN8O12S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 30% PEG 4000, 0.2 M MGCL2, 0.1 M TRIS pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34157 / % possible obs: 99.8 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.046 / Rrim(I) all: 0.165 / Χ2: 1.465 / Net I/σ(I): 6.4 / Num. measured all: 427156
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0312.61.15916730.9340.3341.2070.52399.8
2.03-2.0712.60.99216870.9510.2861.0330.652100
2.07-2.1112.80.93116970.9560.2660.9690.55799.8
2.11-2.1512.80.7616590.970.2180.7910.58199.9
2.15-2.212.70.59816850.9720.1720.6230.60799.9
2.2-2.2512.50.53916850.980.1570.5620.699100
2.25-2.3112.30.45416810.9760.1340.4740.696100
2.31-2.3710.90.38716930.9760.1220.4060.71999.6
2.37-2.4412.30.34216790.9820.1010.3570.75299.9
2.44-2.5213.50.28317170.9890.0790.2940.882100
2.52-2.6113.50.23317000.990.0660.2430.951100
2.61-2.7113.30.21716900.9930.0620.2261.149100
2.71-2.8413.20.17517070.9920.050.1831.27199.9
2.84-2.9913.10.15816760.9940.0450.1651.60999.9
2.99-3.1712.80.13717340.9940.040.1432.02999.8
3.17-3.4211.20.11817010.9940.0370.1242.55399.2
3.42-3.7612.20.09917380.9960.0290.1033.19299.9
3.76-4.3112.60.08417360.9970.0240.0883.49100
4.31-5.4312.10.07717570.9970.0230.083.36799.9
5.43-5011.30.06718620.9980.020.073.10899.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PBO

3pbo


Resolution: 2→33.91 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.665 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 1770 5.2 %RANDOM
Rwork0.1752 ---
obs0.1778 32335 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.62 Å2 / Biso mean: 31.247 Å2 / Biso min: 13.85 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2→33.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 49 193 3820
Biso mean--41.22 38.21 -
Num. residues----473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133751
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173555
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.6485113
X-RAY DIFFRACTIONr_angle_other_deg1.3531.5718226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.925485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21420.612196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68515603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4941531
X-RAY DIFFRACTIONr_chiral_restr0.080.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024269
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02780
LS refinement shellResolution: 2.001→2.053 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 141 -
Rwork0.201 2169 -
all-2310 -
obs--91.96 %

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