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- PDB-6un3: Crystal structure of Pseudomonas aeruginosa PBP3 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6un3
TitleCrystal structure of Pseudomonas aeruginosa PBP3 in complex with ticarcillin
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-XT8 / Peptidoglycan D,D-transpeptidase FtsI / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.5Nov 6, 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)58,1574
Polymers57,6391
Non-polymers5193
Water5,134285
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)68.790, 83.260, 89.220
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-XT8 / (2R,4S)-2-[(1R)-1-{[(2R)-2-carboxy-2-(thiophen-3-yl)acetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / ticarcillin


Mass: 386.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N2O6S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 3350 0.2M CaOAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→60.872 Å / Num. all: 35128 / Num. obs: 35128 / % possible obs: 86.5 % / Redundancy: 5.3 % / Rpim(I) all: 0.057 / Rrim(I) all: 0.143 / Rsym value: 0.13 / Net I/av σ(I): 3.7 / Net I/σ(I): 6.5 / Num. measured all: 187384
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-25.20.6431.12711852530.2950.7150.643289.4
2-2.125.40.4921.52659949630.2160.5430.4922.689
2.12-2.275.10.3531.92293045270.160.3920.3533.587.1
2.27-2.455.20.2722.42212442850.1220.3020.2724.587.5
2.45-2.695.60.2063.12174638880.0880.2260.206686.6
2.69-35.40.1543.81862534800.0680.170.1547.685.5
3-3.475.50.1151700230870.0470.1210.1110.885.1
3.47-4.255.70.08461441625470.0350.0910.0841583
4.25-6.015.40.0696.81082519910.0310.0770.06915.682.4
6.01-45.5865.40.04412.8599911070.020.0490.04415.180

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OC2

3oc2


Resolution: 1.9→45.63 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.756 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 1772 5.1 %RANDOM
Rwork0.2006 ---
obs0.2039 33310 85.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.26 Å2 / Biso mean: 33.111 Å2 / Biso min: 16.24 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2--1.03 Å2-0 Å2
3----2.57 Å2
Refinement stepCycle: final / Resolution: 1.9→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3802 0 32 289 4123
Biso mean--31.34 38.75 -
Num. residues----502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133909
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173722
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.6565311
X-RAY DIFFRACTIONr_angle_other_deg1.2821.5818585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3395500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20720.657198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16715630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3411536
X-RAY DIFFRACTIONr_chiral_restr0.0750.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024419
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02828
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 136 -
Rwork0.362 2520 -
all-2656 -
obs--88.83 %

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