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- PDB-1pyy: Double mutant PBP2x T338A/M339F from Streptococcus pneumoniae str... -

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Basic information

Entry
Database: PDB / ID: 1pyy
TitleDouble mutant PBP2x T338A/M339F from Streptococcus pneumoniae strain R6 at 2.4 A resolution
ComponentsPenicillin-binding protein 2X
KeywordsTRANSPEPTIDASE / PENICILLIN-BINDING PROTEIN / ANTIBIOTIC RESISTANCE / PEPTIDOGLYCAN SYNTHESIS / CELL WALL / TRANSMEMBRANE
Function / homology
Function and homology information


penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / response to antibiotic / plasma membrane
Similarity search - Function
PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase ...PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
octanoyl-sucrose, esterificated at fructose C6 / Penicillin-binding protein 2X
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsChesnel, L. / Pernot, L. / Lemaire, D. / Champelovier, D. / Croize, J. / Dideberg, O. / Vernet, T. / Zapun, A.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: The Structural Modifications Induced by the M339F Substitution in PBP2x from Streptococcus pneumoniae Further Decreases the Susceptibility to beta-Lactams of Resistant Strains
Authors: Chesnel, L. / Pernot, L. / Lemaire, D. / Champelovier, D. / Croize, J. / Dideberg, O. / Vernet, T. / Zapun, A.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: CRYSTAL STRUCTURE OF PBP2X FROM A HIGHLY PENICILLIN-RESISTANT STREPTOCOCCUS PNEUMONIAE CLINICAL ISOLATE
Authors: DESSEN, A. / MOUZ, N. / Gordon, E. / HOPKINS, J. / DIDEBERG, O.
#2: Journal: J.Mol.Biol. / Year: 2000
Title: THE CRYSTAL STRUCTURE OF THE PENICILLIN BINDING PROTEIN 2X FROM STREPTOCOCCUS PNEUMONIAE AND ITS ACYL-ENZYME FORM: IMPLICATION IN DRUG RESISTANCE
Authors: GORDON, E. / MOUZ, N. / DUEE, E. / DIDEBERG, O.
#3: Journal: Nat.Struct.Biol. / Year: 1996
Title: X-RAY STRUCTURE OF STREPTOCOCCUS PNEUMONIAE PBP2X, A PRIMARY PENICILLIN TARGET ENZYME
Authors: PARES, S. / MOUZ, N. / PETILLOT, Y. / HAKENBECK, R. / DIDEBERG, O.
History
DepositionJul 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN The octanoyl chain is bound to the fructose group instead of the glucose group.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 2X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4774
Polymers76,7941
Non-polymers6833
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.224, 64.746, 146.974
Angle α, β, γ (deg.)90.00, 118.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Penicillin-binding protein 2X / PBP-2X / PBP2X


Mass: 76793.922 Da / Num. of mol.: 1 / Mutation: T338A, M339F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: PBPX / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P59676
#2: Polysaccharide 6-O-octanoyl-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / octanoyl-sucrose / esterificated at fructose C6


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 468.493 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: octanoyl-sucrose, esterificated at fructose C6
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_6*OCCCCCCCC/3=O][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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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: 3.5 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 12% PEG 6000, 100 mM sodium acetate, 200 mM ammonium sulfate, glycyl-glycyl-glycine, n-octanoylsucrose, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris1droppH8.0
2100 mM1dropNaCl
31 mMEDTA1drop
412 mg/mlprotein1drop
514 %PEG60001reservoir
6100 mMsodium acetate1reservoirpH4.6
7200 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.99987 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.42→31 Å / Num. obs: 40275 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 29.7
Reflection shellResolution: 2.42→2.55 Å / Redundancy: 6 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 3.5 / % possible all: 98.2
Reflection
*PLUS
Num. measured all: 299369
Reflection shell
*PLUS
% possible obs: 98.2 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QME

1qme


Resolution: 2.42→30.69 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1610393.46 / Data cutoff high rms absF: 1610393.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2014 5 %RANDOM
Rwork0.218 ---
all0.244 ---
obs0.218 40275 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.2897 Å2 / ksol: 0.32268 e/Å3
Displacement parametersBiso mean: 52.4 Å2
Baniso -1Baniso -2Baniso -3
1-10.49 Å20 Å28.58 Å2
2---2.04 Å20 Å2
3----8.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.42→30.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 0 45 241 4928
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it2.772
X-RAY DIFFRACTIONc_mcangle_it4.162.5
X-RAY DIFFRACTIONc_scbond_it4.012.5
X-RAY DIFFRACTIONc_scangle_it5.383
LS refinement shellResolution: 2.42→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 277 4.9 %
Rwork0.283 5327 -
obs--81.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4OSUCROSE.PARAMOSUCROSE.TOP
X-RAY DIFFRACTION5MPD_CNS.PARAMMPD_CNS.TOP
Refinement
*PLUS
Lowest resolution: 31 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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