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- PDB-5oj0: Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoni... -

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Basic information

Entry
Database: PDB / ID: 5oj0
TitlePenicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae in complex with Cefepime
ComponentsPenicillin-binding protein 2X
KeywordsANTIBIOTIC / Penicillin / b-lactam / cell-wall / transpeptidase
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, 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
Cefepime / PASTA domain-containing protein / Penicillin-binding protein 2X
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsBernardo-Garcia, N. / Hermoso, J.A.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Allostery, Recognition of Nascent Peptidoglycan, and Cross-linking of the Cell Wall by the Essential Penicillin-Binding Protein 2x of Streptococcus pneumoniae.
Authors: Bernardo-Garcia, N. / Mahasenan, K.V. / Batuecas, M.T. / Lee, M. / Hesek, D. / Petrackova, D. / Doubravova, L. / Branny, P. / Mobashery, S. / Hermoso, J.A.
History
DepositionJul 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,2902
Polymers76,8081
Non-polymers4821
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area30110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.547, 99.547, 189.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 76807.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: pbpX, spr0304 / Production host: Escherichia coli (E. coli) / References: UniProt: P59676, UniProt: A0A0E8T757*PLUS
#2: Chemical ChemComp-9WT / Cefepime / Cefepime


Mass: 481.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25N6O5S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 3.43 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 2.3-3.0 M NaCl, 0.1 M sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97947 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.66→39.24 Å / Num. obs: 31872 / % possible obs: 99.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.12 / Net I/σ(I): 5.7
Reflection shellResolution: 2.66→2.76 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.8 / Rpim(I) all: 0.69 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1k25

1k25


Resolution: 2.66→39.24 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.188 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.354 / ESU R Free: 0.262 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23143 1621 5.1 %RANDOM
Rwork0.17165 ---
obs0.17477 30354 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 64.555 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.46 Å2
Refinement stepCycle: 1 / Resolution: 2.66→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5057 0 32 212 5301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.025179
X-RAY DIFFRACTIONr_bond_other_d0.0020.024721
X-RAY DIFFRACTIONr_angle_refined_deg2.0131.9677020
X-RAY DIFFRACTIONr_angle_other_deg1.189311026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4095655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.38725.833228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.8515897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1921519
X-RAY DIFFRACTIONr_chiral_restr0.1250.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215775
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02957
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_it6.6116.3182629
X-RAY DIFFRACTIONr_mcbond_other6.6066.3172628
X-RAY DIFFRACTIONr_mcangle_it9.6379.4673281
X-RAY DIFFRACTIONr_mcangle_other9.6369.4683282
X-RAY DIFFRACTIONr_scbond_it7.0036.9392550
X-RAY DIFFRACTIONr_scbond_other7.0026.9412551
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.20510.23738
X-RAY DIFFRACTIONr_long_range_B_refined13.93575.5075677
X-RAY DIFFRACTIONr_long_range_B_other13.93675.5335678
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.66→2.729 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.191 135 -
Rwork0.111 2192 -
obs--99.87 %

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