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- PDB-1rp5: PBP2x from Streptococcus pneumoniae strain 5259 with reduced susc... -

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Basic information

Entry
Database: PDB / ID: 1rp5
TitlePBP2x from Streptococcus pneumoniae strain 5259 with reduced susceptibility to beta-lactam antibiotics
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
Ubiquitin Ligase Nedd4; Chain: W; - #70 / Alpha-Beta Plaits - #2110 / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Ubiquitin Ligase Nedd4; Chain: W; / Penicillin-binding protein, dimerisation domain ...Ubiquitin Ligase Nedd4; Chain: W; - #70 / Alpha-Beta Plaits - #2110 / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Ubiquitin Ligase Nedd4; Chain: W; / 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 / Single Sheet / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Penicillin-binding protein 2x
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPernot, L. / Chesnel, L. / Legouellec, A. / Croize, J. / Vernet, T. / Dideberg, O. / Dessen, A.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: A PBP2x from a clinical isolate of Streptococcus pneumoniae exhibits an alternative mechanism for reduction of susceptibility to beta-lactam antibiotics.
Authors: Pernot, L. / Chesnel, L. / Le Gouellec, A. / Croize, J. / Vernet, T. / Dideberg, O. / Dessen, A.
#1: 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.
#2: 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.
#3: 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.
#4: 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
DepositionDec 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: penicillin-binding protein 2x
B: penicillin-binding protein 2x
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,0044
Polymers153,8122
Non-polymers1922
Water81145
1
A: penicillin-binding protein 2x
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0022
Polymers76,9061
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: penicillin-binding protein 2x
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0022
Polymers76,9061
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)194.989, 194.989, 154.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein penicillin-binding protein 2x


Mass: 76906.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: 5259 / Gene: PBP2X / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061
References: UniProt: P14677, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 4.76 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: PEG 1500, SODIUM ACETATE, AMMONIUM SULFATE, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal grow
*PLUS
Temperature: 8 ℃ / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114 %PEG15001reservoir
250 mMsodium acetate1reservoirpH4.3
3200 mMammonium sulfate1reservoir
450 mMTris-HCl1droppH8.
5100 mM1dropNaCl
61 mMEDTA1drop
710 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97936 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 17, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 3→42 Å / Num. obs: 57788 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 11.4 % / Rsym value: 0.092 / Net I/σ(I): 29.7
Reflection shellResolution: 3→3.16 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3 / Rsym value: 0.426 / % possible all: 77.2
Reflection
*PLUS
Num. measured all: 657234 / Rmerge(I) obs: 0.092
Reflection shell
*PLUS
% possible obs: 77.2 % / Rmerge(I) obs: 0.426

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Processing

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

1qme


Resolution: 3→42 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 4725 8.2 %RANDOM
Rwork0.231 ---
all0.269 57622 --
obs-52897 96.5 %-
Displacement parametersBiso mean: 59.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10260 0 10 45 10315
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.416 631 8.1 %
Rwork0.36 7127 -
obs-7127 79.1 %
Refinement
*PLUS
Lowest resolution: 42 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96

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