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- PDB-5oau: Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 5oau
TitlePenicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae
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 => GO:0005886 / membrane => GO:0016020 / plasma membrane
Similarity search - Function
PASTA domain profile. / PASTA / PASTA domain / PASTA 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 / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
PASTA domain-containing protein / Penicillin-binding protein 2X
Similarity search - Component
Biological speciesStreptococcus pneumoniae (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 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
DepositionJun 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 2X


Theoretical massNumber of molelcules
Total (without water)76,8081
Polymers76,8081
Non-polymers00
Water4,125229
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 area30700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.260, 100.260, 189.810
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 (unknown) / Gene: pbpX, spr0304 / Production host: Escherichia coli (E. coli) / References: UniProt: P59676, UniProt: A0A0E8T757*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.57 Å3/Da / Density % sol: 65.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 2.3-3.0 M NaCl, 0.1 M sodium acetate

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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: 2.67→34.78 Å / Num. obs: 31872 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.09 / Net I/σ(I): 7.5
Reflection shellResolution: 2.67→2.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.7 / Rpim(I) all: 0.48 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1k25
Resolution: 2.67→34.78 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.889 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.256 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22531 1506 4.7 %RANDOM
Rwork0.17345 ---
obs0.17588 30573 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.804 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.17 Å2
Refinement stepCycle: 1 / Resolution: 2.67→34.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5131 0 0 229 5360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.025219
X-RAY DIFFRACTIONr_bond_other_d0.0020.024760
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.9577069
X-RAY DIFFRACTIONr_angle_other_deg1.056311119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.285664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.58725.801231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94315907
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9031519
X-RAY DIFFRACTIONr_chiral_restr0.1030.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215821
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02970
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_it5.2596.2062665
X-RAY DIFFRACTIONr_mcbond_other5.2596.2042664
X-RAY DIFFRACTIONr_mcangle_it7.8719.33326
X-RAY DIFFRACTIONr_mcangle_other7.879.3023327
X-RAY DIFFRACTIONr_scbond_it5.4646.6942554
X-RAY DIFFRACTIONr_scbond_other5.4646.6912552
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9539.8563743
X-RAY DIFFRACTIONr_long_range_B_refined12.24972.8285625
X-RAY DIFFRACTIONr_long_range_B_other12.24772.8165618
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.67→2.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.158 95 -
Rwork0.098 2256 -
obs--99.83 %

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