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- PDB-7kis: Crystal structure of Pseudomonas aeruginosa PBP2 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7kis
TitleCrystal structure of Pseudomonas aeruginosa PBP2 in complex with WCK 5153
ComponentsPeptidoglycan D,D-transpeptidase MrdA
KeywordsHYDROLASE/Inhibitor/Antibiotic / Inhibitor / cell wall / antibiotic resistance / HYDROLASE / HYDROLASE-Inhibitor-Antibiotic complex
Function / homology
Function and homology information


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 / proteolysis / plasma membrane
Similarity search - Function
Penicillin-binding protein 2 / 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-C9D / Peptidoglycan D,D-transpeptidase MrdA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.869 Å
AuthorsRajavel, M. / van den Akker, F.
CitationJournal: Mbio / Year: 2021
Title: Structural Characterization of Diazabicyclooctane beta-Lactam "Enhancers" in Complex with Penicillin-Binding Proteins PBP2 and PBP3 of Pseudomonas aeruginosa.
Authors: Rajavel, M. / Kumar, V. / Nguyen, H. / Wyatt, J. / Marshall, S.H. / Papp-Wallace, K.M. / Deshpande, P. / Bhavsar, S. / Yeole, R. / Bhagwat, S. / Patel, M. / Bonomo, R.A. / van den Akker, F.
History
DepositionOct 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
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
Revision 1.3Oct 23, 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

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Assembly

Deposited unit
A: Peptidoglycan D,D-transpeptidase MrdA
B: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,4155
Polymers144,6212
Non-polymers7943
Water36020
1
A: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7253
Polymers72,3101
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6902
Polymers72,3101
Non-polymers3791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.018, 75.924, 97.299
Angle α, β, γ (deg.)90.000, 106.730, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 63 through 84 or resid 164...
21(chain B and (resid 63 through 84 or resid 164 through 182 or resid 189 through 621 or resid 1))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 63 through 84 or resid 164...A63 - 84
121(chain A and (resid 63 through 84 or resid 164...A164 - 182
131(chain A and (resid 63 through 84 or resid 164...A189 - 219
141(chain A and (resid 63 through 84 or resid 164...A240 - 544
151(chain A and (resid 63 through 84 or resid 164...A562 - 621
161(chain A and (resid 63 through 84 or resid 164...A1
211(chain B and (resid 63 through 84 or resid 164 through 182 or resid 189 through 621 or resid 1))B63 - 84
221(chain B and (resid 63 through 84 or resid 164 through 182 or resid 189 through 621 or resid 1))B164 - 182
231(chain B and (resid 63 through 84 or resid 164 through 182 or resid 189 through 621 or resid 1))B189 - 621
241(chain B and (resid 63 through 84 or resid 164 through 182 or resid 189 through 621 or resid 1))B1

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Components

#1: Protein Peptidoglycan D,D-transpeptidase MrdA / Penicillin-binding protein 2 / PBP-2


Mass: 72310.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pbpA, mrdA, penA, spoVD / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X6V3, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-C9D / (2S,5R)-1-formyl-N'-[(3R)-pyrrolidine-3-carbonyl]-5-[(sulfooxy)amino]piperidine-2-carbohydrazide / open form - WCK 5153


Mass: 379.389 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H21N5O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.01 Å3/Da / Density % sol: 38.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.2M ammonium acetate, and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.979331 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979331 Å / Relative weight: 1
ReflectionResolution: 2.869→29.67 Å / Num. obs: 23998 / % possible obs: 90.8 % / Redundancy: 3.4 % / CC1/2: 0.978 / Rmerge(I) obs: 0.158 / Net I/σ(I): 5.2
Reflection shellResolution: 2.869→3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.514 / Num. unique obs: 3298 / CC1/2: 0.765 / % possible all: 86.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G9F

6g9f


Resolution: 2.869→29.668 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3165 1184 4.94 %
Rwork0.258 22786 -
obs0.2609 23970 90.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.73 Å2 / Biso mean: 42.8285 Å2 / Biso min: 14.89 Å2
Refinement stepCycle: final / Resolution: 2.869→29.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7012 0 51 20 7083
Biso mean--44.57 30.91 -
Num. residues----898
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2666X-RAY DIFFRACTION7.835TORSIONAL
12B2666X-RAY DIFFRACTION7.835TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8693-2.99970.38371550.3438257884
2.9997-3.15770.38611400.3274297994
3.1577-3.35530.35171360.2932292894
3.3553-3.6140.32921430.2629290892
3.614-3.97690.30821530.2352285392
3.9769-4.55060.27191490.2172289692
4.5506-5.72650.28771650.2224282390
5.7265-29.6680.31331430.2626282187

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