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- PDB-6i1i: Crystal structure of TP domain from Escherichia coli penicillin-b... -

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Basic information

Entry
Database: PDB / ID: 6i1i
TitleCrystal structure of TP domain from Escherichia coli penicillin-binding protein 3 in complex with penicillin
ComponentsPeptidoglycan D,D-transpeptidase FtsI,Peptidoglycan D,D-transpeptidase FtsI
KeywordsPEPTIDE BINDING PROTEIN / penicillin-binding protein / peptidoglycan / Transpeptidase
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
Piperacillin (Open Form) / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBellini, D. / Koekemoer, L. / Newman, H. / 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
DepositionOct 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan D,D-transpeptidase FtsI,Peptidoglycan D,D-transpeptidase FtsI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6492
Polymers37,1291
Non-polymers5201
Water1,36976
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 area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.714, 147.672, 43.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-803-

HOH

21A-845-

HOH

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Components

#1: Protein Peptidoglycan D,D-transpeptidase FtsI,Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein 3 / PBP-3


Mass: 37129.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ftsI, pbpB, Z0094, ECs0088 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AD69, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-JPP / Piperacillin (Open Form)


Mass: 519.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29N5O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 6,000, 0.1 M CaCl2, 15% ethylene glycol and 0.1 M TrisHCl pH 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→43.25 Å / Num. obs: 32743 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rrim(I) all: 0.204 / Net I/σ(I): 6.8
Reflection shellResolution: 1.75→1.78 Å

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
DIALSdata reduction
Aimlessdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BJP

4bjp


Resolution: 1.75→43.25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.286 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24704 1701 5.2 %RANDOM
Rwork0.22015 ---
obs0.22155 31015 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.349 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å20 Å20 Å2
2---0.88 Å2-0 Å2
3----2.03 Å2
Refinement stepCycle: 1 / Resolution: 1.75→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 0 76 2534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192515
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9963421
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7185323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86122.76694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70615409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9181521
X-RAY DIFFRACTIONr_chiral_restr0.10.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211894
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 117 -
Rwork0.342 2066 -
obs--98.33 %

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