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- PDB-6q9n: Crystal structure of PBP2a from MRSA in complex with piperacillin... -

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Basic information

Entry
Database: PDB / ID: 6q9n
TitleCrystal structure of PBP2a from MRSA in complex with piperacillin and quinazolinone
ComponentsPenicillin binding protein 2 prime
KeywordsHYDROLASE / Penicillin Binding Protein
Function / homology
Function and homology information


peptidoglycan L,D-transpeptidase activity / penicillin binding / cell wall organization / response to antibiotic / plasma membrane
Similarity search - Function
NTF2-like; domain 1 / NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / 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 / NTF2-like domain superfamily ...NTF2-like; domain 1 / NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / 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 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Piperacillin (Open Form) / beta-muramic acid / Chem-QLN / Penicillin binding protein 2 prime
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMartinez-Caballero, S. / Batuecas, M.T. / Hermoso, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI116548 United States
CitationJournal: Antimicrob.Agents Chemother. / Year: 2019
Title: The Quinazolinone Allosteric Inhibitor of PBP 2a Synergizes with Piperacillin and Tazobactam against Methicillin-Resistant Staphylococcus aureus.
Authors: Janardhanan, J. / Bouley, R. / Martinez-Caballero, S. / Peng, Z. / Batuecas-Mordillo, M. / Meisel, J.E. / Ding, D. / Schroeder, V.A. / Wolter, W.R. / Mahasenan, K.V. / Hermoso, J.A. / Mobashery, S. / Chang, M.
History
DepositionDec 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 9, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin binding protein 2 prime
B: Penicillin binding protein 2 prime
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,32813
Polymers146,5732
Non-polymers1,75511
Water1,60389
1
A: Penicillin binding protein 2 prime
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7468
Polymers73,2871
Non-polymers1,4597
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Penicillin binding protein 2 prime
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5825
Polymers73,2871
Non-polymers2964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.170, 102.876, 187.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Penicillin binding protein 2 prime


Mass: 73286.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: In chain A, the Ser is attached covalently to piperacillin (PA4 residue 403)
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: mecA, SAV0041 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JPA5
#6: Sugar ChemComp-MUR / beta-muramic acid / muramic acid


Type: D-saccharide, beta linking / Mass: 251.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C9H17NO7
IdentifierTypeProgram
b-D-GlcpN3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
MurSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 99 molecules

#2: Chemical ChemComp-QLN / 3-[2-[(~{E})-2-(4-ethynylphenyl)ethenyl]-4-oxidanylidene-quinazolin-3-yl]benzoic acid


Mass: 392.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H16N2O3
#3: Chemical ChemComp-JPP / Piperacillin (Open Form)


Mass: 519.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29N5O7S
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 1000, sodium chloride, HEPES, cadmium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 2.5→49.55 Å / Num. obs: 55031 / % possible obs: 99.77 % / Redundancy: 13.1 % / Rpim(I) all: 0.032 / Net I/σ(I): 15.9
Reflection shellResolution: 2.5→2.58 Å / Rpim(I) all: 0.49

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZG0

3zg0


Resolution: 2.5→49.55 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.907 / SU B: 16.785 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R: 0.558 / ESU R Free: 0.324 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2855 2763 5 %RANDOM
Rwork0.2213 ---
obs0.22449 55031 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 70.451 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2--8.08 Å20 Å2
3----6.81 Å2
Refinement stepCycle: 1 / Resolution: 2.5→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10269 0 55 89 10413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01310499
X-RAY DIFFRACTIONr_bond_other_d0.0020.0179743
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.65514131
X-RAY DIFFRACTIONr_angle_other_deg1.1321.59922841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.36951273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02925.733525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.487152048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9621524
X-RAY DIFFRACTIONr_chiral_restr0.0490.21372
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211563
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021911
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7077.4295101
X-RAY DIFFRACTIONr_mcbond_other2.7057.4285100
X-RAY DIFFRACTIONr_mcangle_it4.51511.1376371
X-RAY DIFFRACTIONr_mcangle_other4.51511.1376372
X-RAY DIFFRACTIONr_scbond_it2.5627.835398
X-RAY DIFFRACTIONr_scbond_other2.5627.835399
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.50211.5737761
X-RAY DIFFRACTIONr_long_range_B_refined7.15284.31811324
X-RAY DIFFRACTIONr_long_range_B_other7.15284.31911325
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 220 -
Rwork0.385 3807 -
obs--99.7 %

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