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- PDB-9otg: Crystal structure of the transpeptidase domain of PBP2 from Neiss... -

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Basic information

Entry
Database: PDB / ID: 9otg
TitleCrystal structure of the transpeptidase domain of PBP2 from Neisseria gonorrhoeae strain FA19 acylated by piperacillin
ComponentsProbable peptidoglycan D,D-transpeptidase PenA
KeywordsLIGASE / penicillin-binding protein / peptidoglycan transpeptidase / piperacillin
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 / response to antibiotic ...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 / response to antibiotic / 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
Piperacillin (Open Form) / Probable peptidoglycan D,D-transpeptidase PenA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae FA19 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.15 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 27, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,6924
Polymers70,6532
Non-polymers1,0392
Water00
1
A: Probable peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8462
Polymers35,3261
Non-polymers5201
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8462
Polymers35,3261
Non-polymers5201
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.986, 77.962, 87.237
Angle α, β, γ (deg.)90.00, 90.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35326.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae FA19 (bacteria) / Gene: penA / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P08149, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-JPP / Piperacillin (Open Form)


Mass: 519.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H29N5O7S / Feature type: SUBJECT OF INVESTIGATION
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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 35-40% PEG 600 and 0.1 M CHES / PH range: 9.0-9.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→39 Å / Num. obs: 10473 / % possible obs: 99 % / Observed criterion σ(F): 0 / Redundancy: 3.9 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.075 / Net I/σ(I): 11.9
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 4 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1053 / CC1/2: 0.731 / CC star: 0.919 / Rpim(I) all: 0.391

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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: 3.15→39 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.879 / SU B: 64.2 / SU ML: 0.484 / Cross valid method: THROUGHOUT / ESU R Free: 0.602 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.266 537 5.1 %RANDOM
Rwork0.153 ---
obs0.159 9942 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.3 Å2
Baniso -1Baniso -2Baniso -3
1-10.43 Å2-0 Å2-1.27 Å2
2---4.26 Å2-0 Å2
3----6.14 Å2
Refinement stepCycle: 1 / Resolution: 3.15→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 72 0 4930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125034
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164879
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.8436826
X-RAY DIFFRACTIONr_angle_other_deg0.4731.76711211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2935637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.741539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03810821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025949
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021139
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_it4.836.9022560
X-RAY DIFFRACTIONr_mcbond_other4.836.9012560
X-RAY DIFFRACTIONr_mcangle_it7.87212.3893193
X-RAY DIFFRACTIONr_mcangle_other7.87212.3883194
X-RAY DIFFRACTIONr_scbond_it4.8487.4672474
X-RAY DIFFRACTIONr_scbond_other4.8477.4672475
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other813.5523634
X-RAY DIFFRACTIONr_long_range_B_refined11.34865.525706
X-RAY DIFFRACTIONr_long_range_B_other11.34765.525707
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.15→3.23 Å
RfactorNum. reflection% reflection
Rfree0.288 44 -
Rwork0.233 732 -
obs--96.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.534-0.2421-0.12330.7903-0.01840.68490.06490.0281-0.0461-0.0063-0.0981-0.0089-0.0242-0.0170.03320.2135-0.0195-0.04530.01470.00450.013118.2575-10.74115.7285
20.38070.04290.35541.07220.20521.2604-0.0491-0.1020.1011-0.0167-0.03880.07510.0356-0.16370.08790.08820.0066-0.02910.0794-0.03210.0347.95849.996237.8461
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A236 - 601
2X-RAY DIFFRACTION2B234 - 601

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