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

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Basic information

Entry
Database: PDB / ID: 3equ
TitleCrystal structure of penicillin-binding protein 2 from Neisseria gonorrhoeae
ComponentsPenicillin-binding protein 2
KeywordsBIOSYNTHETIC PROTEIN / Penicillin-binding protein / Class B transpeptidase / 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 / 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: Non-polymer description / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)121,03321
Polymers119,2162
Non-polymers1,81719
Water2,630146
1
A: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,56511
Polymers59,6081
Non-polymers95710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,46910
Polymers59,6081
Non-polymers8619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.4, 138.6, 228.0
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: 59607.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: FA19 / 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.: 17 / 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.: 146 / 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: 3.8 Å3/Da / Density % sol: 67.66 %
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: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2001
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→87 Å / Num. all: 73860 / Num. obs: 73860 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 43.2 Å2 / Rsym value: 0.061 / Net I/σ(I): 8.8
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 0 / Num. unique all: 3081 / Rsym value: 0.349 / % possible all: 52.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.4→66.6 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.914 / SU B: 10.749 / SU ML: 0.126 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3467 5.1 %RANDOM
Rwork0.209 ---
all0.211 68535 --
obs0.211 68535 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.52 Å20 Å20 Å2
2--1.25 Å20 Å2
3---1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.4→66.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6516 0 97 146 6759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226724
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9879119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.723.46289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.515.0271107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.71557
X-RAY DIFFRACTIONr_chiral_restr0.0970.21010
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025049
X-RAY DIFFRACTIONr_nbd_refined0.2030.22939
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24543
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2375
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.28
X-RAY DIFFRACTIONr_mcbond_it0.8621.54336
X-RAY DIFFRACTIONr_mcangle_it1.18526796
X-RAY DIFFRACTIONr_scbond_it2.09732636
X-RAY DIFFRACTIONr_scangle_it3.2184.52323
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 192 -
Rwork0.228 3377 -
obs-3569 70 %

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