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

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Basic information

Entry
Database: PDB / ID: 5oiz
TitlePenicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae in complex with oxacillin
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 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 ...: / 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
Chem-1S6 / Penicillin-binding protein 2X
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)77,2112
Polymers76,8081
Non-polymers4031
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area29030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.415, 100.415, 189.799
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 (strain ATCC BAA-255 / R6) (bacteria)
Gene: pbpX, spr0304 / Production host: Escherichia coli (E. coli) / Variant (production host): Rx1 / References: UniProt: P59676
#2: Chemical ChemComp-1S6 / (2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid / Oxacillin, bound form


Mass: 403.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N3O5S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 3.56 Å3/Da / Density % sol: 65.45 %
Crystal growTemperature: 277 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: 0.97924 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: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.7→86.79 Å / Num. obs: 30875 / % possible obs: 99.7 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.078 / Net I/σ(I): 8.5
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4451 / CC1/2: 0.58 / Rpim(I) all: 0.67 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Cootmodel building
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K25

1k25


Resolution: 2.7→48.54 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.963 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28096 1601 5.1 %RANDOM
Rwork0.21656 ---
obs0.21985 29554 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.405 Å2
Baniso -1Baniso -2Baniso -3
1-27.61 Å20 Å20 Å2
2--27.61 Å20 Å2
3----55.22 Å2
Refinement stepCycle: 1 / Resolution: 2.7→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4994 0 28 100 5122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.025112
X-RAY DIFFRACTIONr_bond_other_d0.0030.024656
X-RAY DIFFRACTIONr_angle_refined_deg2.5961.9686930
X-RAY DIFFRACTIONr_angle_other_deg1.387310869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8755648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90425.867225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.50215880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8861518
X-RAY DIFFRACTIONr_chiral_restr0.1510.2785
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215717
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02951
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_it3.0015.0682601
X-RAY DIFFRACTIONr_mcbond_other3.0025.0682600
X-RAY DIFFRACTIONr_mcangle_it3.9117.5993246
X-RAY DIFFRACTIONr_mcangle_other3.917.5993247
X-RAY DIFFRACTIONr_scbond_it3.3685.2072511
X-RAY DIFFRACTIONr_scbond_other3.3655.2062509
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3877.7473684
X-RAY DIFFRACTIONr_long_range_B_refined5.49361.9196084
X-RAY DIFFRACTIONr_long_range_B_other5.49361.9226085
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 129 -
Rwork0.3 2133 -
obs--99.74 %
Refinement TLS params.Method: refined / Origin x: 52.1791 Å / Origin y: -14.7841 Å / Origin z: -1.6388 Å
111213212223313233
T0.1411 Å2-0.001 Å20.0106 Å2-0.1471 Å20.0022 Å2--0.0046 Å2
L0.1644 °20.0515 °20.0428 °2-0.2705 °2-0.0715 °2--0.6226 °2
S0.0038 Å °-0.0357 Å °0.0029 Å °0.005 Å °0.0112 Å °-0.0244 Å °-0.0096 Å °0.0104 Å °-0.015 Å °

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