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- PDB-9z5t: Crystal structure of the transpeptidase domain of PBP2 from the N... -

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Basic information

Entry
Database: PDB / ID: 9z5t
TitleCrystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with boronate inhibitor VNRX-14079
ComponentsProbable peptidoglycan D,D-transpeptidase PenA
KeywordsLIGASE / Neisseria gonorrhoeae / cephalosporin resistance / Penicillin-binding protein 2 / Boronate inhibitor
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / 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
: / Probable peptidoglycan D,D-transpeptidase PenA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsBala, S. / Stratton, C.M. / Davies, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI141239 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI164794 United States
CitationJournal: To Be Published
Title: A new class of penicillin-binding protein inhibitors to address drug-resistant Neisseria gonorrhoeae
Authors: Uehara, T. / Zulli, A.L. / Miller, B. / Avery, L.M. / Boyd, S.A. / Chatwin, C.L. / Chu, G.H. / Drager, A. / Edwards, M. / Hart, S.E. / Myers, C.L. / Rongola, G. / Stevenson, A. / Uehara, K. ...Authors: Uehara, T. / Zulli, A.L. / Miller, B. / Avery, L.M. / Boyd, S.A. / Chatwin, C.L. / Chu, G.H. / Drager, A. / Edwards, M. / Hart, S.E. / Myers, C.L. / Rongola, G. / Stevenson, A. / Uehara, K. / Yi, F. / Wang, B. / Liu, Z. / Wang, M. / Zhao, Z. / Zhao, X. / Zhao, H. / Stratton, C.M. / Bala, S. / Davies, C. / Travc, R. / Jerse, A.E. / Pevear, D.C. / Burns, C.J. / Daigle, D.M. / Condon, S.M.
History
DepositionNov 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 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)36,0082
Polymers35,3611
Non-polymers6461
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.865, 60.151, 111.023
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: 35361.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: H041 / Gene: penA / Plasmid: PMALC2KV / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F2Z7K9, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-A1C02 / (3R)-7-fluoro-3-{[(2R)-2-(3-fluoro-4-phosphonophenyl)-2-{[3-(methanesulfonyl)-2-oxoimidazolidine-1-carbonyl]amino}acetyl]amino}-2-hydroxy-3,4-dihydro-2H-1,2-benzoxaborinine-8-carboxylic acid


Mass: 646.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C22H22BF2N4O12PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.41 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.3 / Details: 40% PEG 600, 0.1 M CHES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 5, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 20048 / % possible obs: 99.4 % / Redundancy: 5.9 % / CC1/2: 0.929 / CC star: 0.982 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.082 / Rrim(I) all: 0.199 / Χ2: 1.127 / Net I/σ(I): 8.3 / Num. measured all: 118798
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.1-2.185.60.40119850.8850.9690.1870.4441.11599.7
2.18-2.265.90.41319470.8940.9720.1870.4551.36799.4
2.26-2.375.70.36419870.8710.9650.170.4031.40299.4
2.37-2.495.60.31419470.9110.9760.150.3491.03798.9
2.49-2.655.70.29519800.8770.9670.1390.3281.06499.2
2.65-2.856.50.25119780.9510.9870.1060.2731.04799.5
2.85-3.146.40.20720090.9620.990.0880.2261.04299.6
3.14-3.596.30.17520160.9350.9830.0760.1911.09299.3
3.59-4.525.50.12620330.9740.9930.0580.1391.10799.2
4.52-505.90.09421660.8940.9710.0440.1041.03499.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→40.83 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.905 / SU B: 4.927 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 981 4.9 %RANDOM
Rwork0.191 ---
obs0.193 19019 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å2-0 Å2
2--0.74 Å20 Å2
3---0.31 Å2
Refinement stepCycle: 1 / Resolution: 2.1→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 43 77 2550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122540
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162457
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.8353455
X-RAY DIFFRACTIONr_angle_other_deg0.5771.7565657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0275323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.95516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76310420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022948
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02554
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_it1.5531.9211286
X-RAY DIFFRACTIONr_mcbond_other1.5511.9211286
X-RAY DIFFRACTIONr_mcangle_it2.3653.4381605
X-RAY DIFFRACTIONr_mcangle_other2.3653.441606
X-RAY DIFFRACTIONr_scbond_it2.3572.2981254
X-RAY DIFFRACTIONr_scbond_other2.3382.2961246
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8844.0881849
X-RAY DIFFRACTIONr_long_range_B_refined5.15419.272829
X-RAY DIFFRACTIONr_long_range_B_other5.13419.212820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 73 -
Rwork0.21 1372 -
obs--98.5 %

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