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- PDB-3eqv: Crystal structure of penicillin-binding protein 2 from Neisseria ... -

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Basic information

Entry
Database: PDB / ID: 3eqv
TitleCrystal structure of penicillin-binding protein 2 from Neisseria gonorrhoeae containing four mutations associated with penicillin resistance
ComponentsPenicillin-binding protein 2
KeywordsBIOSYNTHETIC PROTEIN / Penicillin-binding protein / Class B transpeptidase / penicillin resistance / Cell division / Cell inner membrane / Cell membrane / Cell shape / Cell wall biogenesis/degradation / Peptidoglycan synthesis
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / 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 / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / plasma membrane
Similarity search - Function
Beta-Lactamase - #330 / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / 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 ...Beta-Lactamase - #330 / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / 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 / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Alpha-Beta Complex / 2-Layer Sandwich / 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 / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsPowell, A.J. / Deacon, A.M. / Nicholas, R.A. / Davies, C.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal Structures of Penicillin-binding Protein 2 from Penicillin-susceptible and -resistant Strains of Neisseria gonorrhoeae Reveal an Unexpectedly Subtle Mechanism for Antibiotic Resistance.
Authors: Powell, A.J. / Tomberg, J. / Deacon, A.M. / Nicholas, R.A. / Davies, C.
History
DepositionOct 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-binding protein 2
B: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,84319
Polymers118,2182
Non-polymers1,62517
Water1,42379
1
A: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7778
Polymers59,1091
Non-polymers6687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,06611
Polymers59,1091
Non-polymers95710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Penicillin-binding protein 2
hetero molecules

B: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,84319
Polymers118,2182
Non-polymers1,62517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area5020 Å2
ΔGint-153 kcal/mol
Surface area37520 Å2
MethodPISA
4
B: Penicillin-binding protein 2
hetero molecules

A: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,84319
Polymers118,2182
Non-polymers1,62517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area3520 Å2
ΔGint-153 kcal/mol
Surface area39020 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-148 kcal/mol
Surface area39230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.6, 137.2, 229.8
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 Penicillin-binding protein 2 / PBP-2


Mass: 59108.957 Da / Num. of mol.: 2 / Mutation: F504L, A510V, A516G, P551S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: 6140 / Gene: penA / Plasmid: pMAL-C2KV/H6 / Production host: Escherichia coli (E. coli) / Strain (production host): GW6011
References: UniProt: P08149, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3.84 Å3/Da / Density % sol: 67.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.2 M ammonium sulphate, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97934 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 11, 2006
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 71399 / Num. obs: 71399 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 49.1 Å2 / Rsym value: 0.101 / Net I/σ(I): 29.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 5957 / Rsym value: 0.52 / % possible all: 83.5

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Processing

Software
NameVersionClassification
MAR345softwaredata collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Wild-type structure

Resolution: 2.4→48.1 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.921 / SU B: 15.651 / SU ML: 0.171 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3558 5 %RANDOM
Rwork0.217 ---
all0.219 71366 --
obs0.219 71366 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2---0.15 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6633 0 87 79 6799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226836
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9839267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6923.5300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.0915.0261135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.831558
X-RAY DIFFRACTIONr_chiral_restr0.0920.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025141
X-RAY DIFFRACTIONr_nbd_refined0.20.22843
X-RAY DIFFRACTIONr_nbtor_refined0.2960.24601
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.212
X-RAY DIFFRACTIONr_mcbond_it0.6041.54404
X-RAY DIFFRACTIONr_mcangle_it1.03826898
X-RAY DIFFRACTIONr_scbond_it1.61432685
X-RAY DIFFRACTIONr_scangle_it2.5934.52367
LS refinement shellResolution: 2.4→2.454 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 209 -
Rwork0.267 3973 -
obs-4182 80.4 %

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