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- PDB-6p53: Crystal structure of the transpeptidase domain of PBP2 from Neiss... -

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Basic information

Entry
Database: PDB / ID: 6p53
TitleCrystal structure of the transpeptidase domain of PBP2 from Neisseria gonorrhoeae in apo form
Componentspeptidoglycan D,D-transpeptidase PenA
KeywordsHYDROLASE / Penicillin-binding protein / transpeptidase domain / N. gonorrhoeae / 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 / response to antibiotic ...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 / 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 / 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
PHOSPHATE ION / Probable peptidoglycan D,D-transpeptidase PenA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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: 2019
Title: Recognition of the beta-lactam carboxylate triggers acylation ofNeisseria gonorrhoeaepenicillin-binding protein 2.
Authors: Singh, A. / Tomberg, J. / Nicholas, R.A. / Davies, C.
History
DepositionMay 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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: peptidoglycan D,D-transpeptidase PenA
B: peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7473
Polymers70,6532
Non-polymers951
Water3,927218
1
A: peptidoglycan D,D-transpeptidase PenA


Theoretical massNumber of molelcules
Total (without water)35,3261
Polymers35,3261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4212
Polymers35,3261
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.334, 77.254, 88.007
Angle α, β, γ (deg.)90.00, 91.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35326.262 Da / Num. of mol.: 2 / Fragment: UNP residues 237-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: penA / Plasmid: pMAL-C2KV / Production host: Escherichia coli (E. coli) / Strain (production host): GW6011
References: UniProt: P08149, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.3 / Details: 40% PEG600, 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: Feb 20, 2018
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: 1.92→36.09 Å / Num. obs: 42141 / % possible obs: 90.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.022 / Net I/σ(I): 33.9
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2272 / CC1/2: 0.93 / Rpim(I) all: 0.191 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4U3T

4u3t


Resolution: 1.92→36.09 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.982 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.165 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1987 4.7 %RANDOM
Rwork0.181 ---
obs0.184 40127 90.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.881 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å2-0 Å20.82 Å2
2---0.91 Å20 Å2
3----1.58 Å2
Refinement stepCycle: 1 / Resolution: 1.92→36.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 5 218 5083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195027
X-RAY DIFFRACTIONr_bond_other_d0.0010.024796
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9676827
X-RAY DIFFRACTIONr_angle_other_deg0.803311101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2925655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92422.864206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55815836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7131542
X-RAY DIFFRACTIONr_chiral_restr0.0860.2769
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215629
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021029
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_it2.0243.2312575
X-RAY DIFFRACTIONr_mcbond_other2.0233.232574
X-RAY DIFFRACTIONr_mcangle_it2.9924.833218
X-RAY DIFFRACTIONr_mcangle_other2.9924.833219
X-RAY DIFFRACTIONr_scbond_it2.3653.6072452
X-RAY DIFFRACTIONr_scbond_other2.3643.6022448
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7535.2813594
X-RAY DIFFRACTIONr_long_range_B_refined5.23838.4785522
X-RAY DIFFRACTIONr_long_range_B_other5.21838.3855492
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.919→1.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 167 -
Rwork0.248 3082 -
obs--94.89 %

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