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- PDB-9osl: Crystal structure of the transpeptidase domain of a Y422A mutant ... -

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Basic information

Entry
Database: PDB / ID: 9osl
TitleCrystal structure of the transpeptidase domain of a Y422A mutant of PBP2 from Neisseria gonorrhoeae strain H041 acylated by ceftriaxone
ComponentsProbable peptidoglycan D,D-transpeptidase PenA
KeywordsLIGASE / penicillin-binding protein / peptidoglycan transpeptidase / ceftriaxone
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / FtsZ-dependent cytokinesis / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane
Similarity search - Function
Peptidoglycan D,D-transpeptidase FtsI / 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
CEFOTAXIME, C3' cleaved, open, bound form / TRIETHYLENE GLYCOL / Probable peptidoglycan D,D-transpeptidase PenA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsStratton, C.M. / Bala, S. / Davies, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI164794 United States
CitationJournal: To Be Published
Title: Tyrosine-422 plays a crucial role in acylation and transpeptidation in penicillin-binding protein 2 from Neisseria gonorrhoeae
Authors: Stratton, C.M. / Bala, S. / Bivins, M.M. / Nicholas, R.A. / Davies, C.
History
DepositionMay 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9094
Polymers35,2691
Non-polymers6403
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.771, 59.450, 112.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable peptidoglycan D,D-transpeptidase PenA / Penicillin-binding protein 2 / PBP-2


Mass: 35269.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: H041 / Gene: penA / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: F2Z7K9, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form


Mass: 397.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C14H15N5O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 45.5 % / Description: Plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M CHES buffer, pH 9.1 to 10.1, and 32-42% PEG 600.
PH range: 9.3-10.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 13460 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Redundancy: 6.9 % / CC1/2: 0.985 / CC star: 0.966 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.052 / Χ2: 0.511 / Net I/σ(I): 8.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 2 / Num. unique obs: 613 / CC1/2: 0.902 / CC star: 0.974 / Rpim(I) all: 0.139 / Χ2: 0.32 / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→40.98 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.047 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.448 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.243 689 5.1 %RANDOM
Rwork0.19 ---
obs0.199 12720 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.97 Å2-0 Å2-0 Å2
2---1.84 Å2-0 Å2
3---4.81 Å2
Refinement stepCycle: 1 / Resolution: 2.4→40.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 42 12 2500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122537
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162471
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.8323436
X-RAY DIFFRACTIONr_angle_other_deg0.571.7515687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0735323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.603515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46610419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022938
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02547
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_it2.6553.2321295
X-RAY DIFFRACTIONr_mcbond_other2.6353.2331295
X-RAY DIFFRACTIONr_mcangle_it4.1985.7961617
X-RAY DIFFRACTIONr_mcangle_other4.1975.8011618
X-RAY DIFFRACTIONr_scbond_it3.7863.8241242
X-RAY DIFFRACTIONr_scbond_other3.7843.8241243
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1196.7971820
X-RAY DIFFRACTIONr_long_range_B_refined7.68130.642731
X-RAY DIFFRACTIONr_long_range_B_other7.6830.632732
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.455 Å
RfactorNum. reflection% reflection
Rfree0.304 41 -
Rwork0.265 831 -
obs--86.85 %

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