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- PDB-6un1: Crystal structure of Pseudomonas aeruginosa PBP3 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6un1
TitleCrystal structure of Pseudomonas aeruginosa PBP3 in complex with temocillin
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE / temocillin / ticarcillin / pseudomonas aeruginosa PBP3 / penicillin-binding protein 3 / transpeptidase / HMM / high-molecular mass / b-lactam / lactam / penicillin
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / 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-TJ7 / Peptidoglycan D,D-transpeptidase FtsI / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsSacco, M. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI147654 United States
CitationJournal: Antimicrob.Agents Chemother. / Year: 2019
Title: Influence of the alpha-Methoxy Group on the Reaction of Temocillin with Pseudomonas aeruginosa PBP3 and CTX-M-14 beta-Lactamase.
Authors: Sacco, M.D. / Kroeck, K.G. / Kemp, M.T. / Zhang, X. / Andrews, L.D. / Chen, Y.
History
DepositionOct 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,0552
Polymers57,6391
Non-polymers4161
Water3,639202
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)67.126, 81.712, 88.082
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: 57638.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: pbpB, ftsI, ftsI_1, ftsI_2, ALP65_00912, CAZ10_21230, CGU42_01090, DZ934_06595, DZ962_00565, E4V10_06485, EFK68_01815, IPC1492_18840, IPC3_13380, IPC605_16140, IPC669_10550, PAERUG_E15_London_ ...Gene: pbpB, ftsI, ftsI_1, ftsI_2, ALP65_00912, CAZ10_21230, CGU42_01090, DZ934_06595, DZ962_00565, E4V10_06485, EFK68_01815, IPC1492_18840, IPC3_13380, IPC605_16140, IPC669_10550, PAERUG_E15_London_28_01_14_00534, RW109_RW109_05757
Production host: Escherichia coli (E. coli)
References: UniProt: Q51504, UniProt: G3XD46*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-TJ7 / (2R,4S)-2-[(1S)-1-{[(2R)-2-carboxy-2-(thiophen-3-yl)acetyl]amino}-1-methoxy-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4 -carboxylic acid / temocillin


Mass: 416.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N2O7S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350 0.2 M CaOAc

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 22516 / % possible obs: 97.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.052 / Rrim(I) all: 0.107 / Χ2: 0.911 / Net I/σ(I): 6.8 / Num. measured all: 89234
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.293.80.69210880.6520.3970.8020.89696.3
2.29-2.333.80.59410820.7880.340.6870.9195.6
2.33-2.383.80.5910940.7740.330.6790.89895.5
2.38-2.423.80.57110680.8290.3190.6570.89995.7
2.42-2.483.90.48911060.8880.2720.5620.90195.4
2.48-2.533.90.40510770.8950.2270.4660.89495
2.53-2.63.90.37910710.9080.2090.4340.93294.6
2.6-2.6740.32810980.9250.1820.3770.97895
2.67-2.7540.28610920.9410.1580.3280.98395
2.75-2.8340.26411070.9440.1450.3020.93995.1
2.83-2.9440.21810760.9620.120.250.97596.5
2.94-3.0540.16211390.9740.0890.1850.97797.9
3.05-3.1940.12911410.9810.0710.1480.93999.2
3.19-3.364.10.10211520.9890.0570.1180.92599.7
3.36-3.574.10.07311590.9940.040.0840.92499.9
3.57-3.854.10.06311680.9940.0340.0720.997100
3.85-4.234.10.04911690.9970.0270.0560.921100
4.23-4.854.10.03911870.9970.0220.0450.81199.8
4.85-6.140.03611960.9980.020.0410.63399.7
6.1-503.70.03612460.9960.0210.0420.90596.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OC2

3oc2


Resolution: 2.26→33.59 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.451 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.358 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 1059 4.7 %RANDOM
Rwork0.17 ---
obs0.1731 21244 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.64 Å2 / Biso mean: 35.684 Å2 / Biso min: 19.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å2-0 Å2
2---0.32 Å2-0 Å2
3----0.17 Å2
Refinement stepCycle: final / Resolution: 2.26→33.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 27 204 4027
Biso mean--31.47 38.72 -
Num. residues----502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133943
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173756
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.6575365
X-RAY DIFFRACTIONr_angle_other_deg1.2781.5828665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5775508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.79820.606198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12215638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.351536
X-RAY DIFFRACTIONr_chiral_restr0.0870.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024478
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02841
LS refinement shellResolution: 2.262→2.321 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 48 -
Rwork0.225 1374 -
all-1422 -
obs--84.24 %

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