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- PDB-6vbl: Crystal structure of the transpeptidase domain of PBP2 from the N... -

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Basic information

Entry
Database: PDB / ID: 6vbl
TitleCrystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin decreased susceptibility strain 35/02
ComponentsProbable peptidoglycan D,D-transpeptidase PenA
KeywordsHYDROLASE / PENICILLIN-BINDING PROTEIN / TRANSPEPTIDASE DOMAIN / ANTIBIOTIC RESISTANCE
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like ...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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable peptidoglycan D,D-transpeptidase PenA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsSingh, A. / Davies, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM066861 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Mutations in Neisseria gonorrhoeae penicillin-binding protein 2 associated with extended-spectrum cephalosporin resistance create an energetic barrier against acylation via restriction of protein dynamics
Authors: Singh, A. / Turner, J. / Tomberg, J. / Fedarovich, A. / Unemo, M. / Nicholas, R.A. / Davies, C.
History
DepositionDec 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,3311
Polymers35,3311
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.621, 61.085, 109.140
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: 35331.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: penA / Plasmid: pMALC2KV / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8RR30, serine-type D-Ala-D-Ala carboxypeptidase
#2: 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: 2.42 Å3/Da / Density % sol: 49.16 %
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: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2019
RadiationMonochromator: double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→31.72 Å / Num. obs: 26212 / % possible obs: 99.5 % / Redundancy: 8.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.05 / Net I/σ(I): 35.7
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 9 % / Rmerge(I) obs: 0.979 / Mean I/σ(I) obs: 7.2 / Num. unique obs: 1285 / CC1/2: 0.658 / Rpim(I) all: 0.349 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P53

6p53


Resolution: 1.93→31.72 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.657 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.129
RfactorNum. reflection% reflectionSelection details
Rfree0.20532 1293 4.9 %RANDOM
Rwork0.18296 ---
obs0.18407 24878 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.133 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å2-0 Å2
2---0.28 Å2-0 Å2
3---0.55 Å2
Refinement stepCycle: 1 / Resolution: 1.93→31.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 0 100 2550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192509
X-RAY DIFFRACTIONr_bond_other_d0.0010.022407
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9653405
X-RAY DIFFRACTIONr_angle_other_deg0.73735573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7225327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40423.57995
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83315425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4881515
X-RAY DIFFRACTIONr_chiral_restr0.0770.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212786
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
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_it1.6023.3321299
X-RAY DIFFRACTIONr_mcbond_other1.5883.3291298
X-RAY DIFFRACTIONr_mcangle_it2.4074.9881623
X-RAY DIFFRACTIONr_mcangle_other2.4074.991624
X-RAY DIFFRACTIONr_scbond_it2.2833.7621210
X-RAY DIFFRACTIONr_scbond_other2.2823.7631211
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7535.5051781
X-RAY DIFFRACTIONr_long_range_B_refined4.89140.2482790
X-RAY DIFFRACTIONr_long_range_B_other4.86940.1852779
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.977 Å
RfactorNum. reflection% reflection
Rfree0.205 97 -
Rwork0.176 1793 -
obs--99.42 %

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