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- PDB-1k25: PBP2x from a Highly Penicillin-resistant Streptococcus pneumoniae... -

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Basic information

Entry
Database: PDB / ID: 1k25
TitlePBP2x from a Highly Penicillin-resistant Streptococcus pneumoniae Clinical Isolate
Componentslow-affinity PENICILLIN-BINDING PROTEIN 2X
KeywordsMEMBRANE PROTEIN / antibiotic resistance / clinical mutant / low-affinity penicillin-binding
Function / homology
Function and homology information


penicillin binding / regulation of cell shape / membrane => GO:0016020 / cell cycle / cell division / 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
Low-affinity penicillin-binding protein 2X
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDessen, A. / Mouz, N. / Hopkins, J. / Dideberg, O.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of PBP2x from a highly penicillin-resistant Streptococcus pneumoniae clinical isolate: a mosaic framework containing 83 mutations.
Authors: Dessen, A. / Mouz, N. / Gordon, E. / Hopkins, J. / Dideberg, O.
History
DepositionSep 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: low-affinity PENICILLIN-BINDING PROTEIN 2X
B: low-affinity PENICILLIN-BINDING PROTEIN 2X
C: low-affinity PENICILLIN-BINDING PROTEIN 2X
D: low-affinity PENICILLIN-BINDING PROTEIN 2X


Theoretical massNumber of molelcules
Total (without water)301,0384
Polymers301,0384
Non-polymers00
Water37821
1
A: low-affinity PENICILLIN-BINDING PROTEIN 2X


Theoretical massNumber of molelcules
Total (without water)75,2591
Polymers75,2591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: low-affinity PENICILLIN-BINDING PROTEIN 2X


Theoretical massNumber of molelcules
Total (without water)75,2591
Polymers75,2591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: low-affinity PENICILLIN-BINDING PROTEIN 2X


Theoretical massNumber of molelcules
Total (without water)75,2591
Polymers75,2591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: low-affinity PENICILLIN-BINDING PROTEIN 2X


Theoretical massNumber of molelcules
Total (without water)75,2591
Polymers75,2591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.560, 146.560, 132.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
low-affinity PENICILLIN-BINDING PROTEIN 2X / PBP2X


Mass: 75259.430 Da / Num. of mol.: 4 / Mutation: F364L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: O34006
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: PEG 2000, ammonium sulfate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 15K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 Msodium acetate1reservoir
222-24 %PEG20001reservoir
3200 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. all: 52413 / Num. obs: 46531 / % possible obs: 96.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.11
Reflection shellResolution: 3.2→3.4 Å / Rmerge(I) obs: 0.36 / % possible all: 97.8
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 167780
Reflection shell
*PLUS
% possible obs: 97.8 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→19.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2685804.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.312 4672 10 %RANDOM
Rwork0.235 ---
obs0.235 46531 89 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.226671 e/Å3
Displacement parametersBiso mean: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.6 Å212.19 Å20 Å2
2--5.6 Å20 Å2
3----11.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.77 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3.2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16765 0 0 21 16786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 826 10.4 %
Rwork0.323 7130 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99
LS refinement shell
*PLUS
Rfactor Rfree: 0.392 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.323

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