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- PDB-6r40: Apo structure of R504C mutant of Pseudomonas aeruginosa Penicilli... -

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Basic information

Entry
Database: PDB / ID: 6r40
TitleApo structure of R504C mutant of Pseudomonas aeruginosa Penicillin-Binding Protein 3 (PBP3)
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE / penicillin-binding protein / peptidoglycan / Transpeptidase
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 / proteolysis / plasma membrane
Similarity search - Function
Beta-Lactamase - #330 / 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 - #330 / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBellini, D. / Dowson, C.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)grant.MR/P007503/1 United Kingdom
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam ...Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam Target-Mediated Resistance.
Authors: Bellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G.
History
DepositionMar 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Data collection / Database references / Category: database_2 / reflns / reflns_shell
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan D,D-transpeptidase FtsI


Theoretical massNumber of molelcules
Total (without water)57,9731
Polymers57,9731
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.530, 83.830, 89.690
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 Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein 3 / PBP-3


Mass: 57972.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: ftsI, pbpB, PA4418 / Production host: Escherichia coli (E. coli)
References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% (w/v) polyethylene glycol 3 350, 0.1 M Bis-Tris propane pH 7.8 and 1% (w/v) protamine sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→61.24 Å / Num. obs: 25878 / % possible obs: 100 % / Redundancy: 11.8 % / CC1/2: 1 / Rrim(I) all: 0.15 / Net I/σ(I): 13.1
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 1072 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OC2

3oc2


Resolution: 2.2→61.24 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.805 / SU B: 10.701 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30797 1306 5.1 %RANDOM
Rwork0.24023 ---
obs0.24365 24521 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.459 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å2-0 Å2-0 Å2
2--0.98 Å2-0 Å2
3----3.33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→61.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3850 0 0 54 3904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193920
X-RAY DIFFRACTIONr_bond_other_d0.0020.023838
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9665316
X-RAY DIFFRACTIONr_angle_other_deg1.0738801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6235502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98823.313166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00215649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3641535
X-RAY DIFFRACTIONr_chiral_restr0.1270.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214460
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02881
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_it3.735.3482017
X-RAY DIFFRACTIONr_mcbond_other3.7055.3462016
X-RAY DIFFRACTIONr_mcangle_it5.72782516
X-RAY DIFFRACTIONr_mcangle_other5.7278.0032517
X-RAY DIFFRACTIONr_scbond_it3.4695.7811903
X-RAY DIFFRACTIONr_scbond_other3.4685.7841904
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.428.5192801
X-RAY DIFFRACTIONr_long_range_B_refined8.71262.3584139
X-RAY DIFFRACTIONr_long_range_B_other8.71762.3824135
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 81 -
Rwork0.444 1130 -
obs--61.88 %

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