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- PDB-6hr4: Apo form of penicillin-binding protein 3 from P. aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6hr4
TitleApo form of penicillin-binding protein 3 from P. aeruginosa
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsPENICILLIN-BINDING PROTEIN / penicillin-binding protein peptidoglycan / Hydrolase
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / FtsZ-dependent cytokinesis / 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 ...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 PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 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: To Be Published
Title: Apo form of penicillin-binding protein 3 from P. aeruginosa
Authors: Bellini, D. / Dowson, C.G.
History
DepositionSep 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 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


Theoretical massNumber of molelcules
Total (without water)57,8731
Polymers57,8731
Non-polymers00
Water11,313628
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 area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.548, 82.140, 88.113
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: 57872.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 / Gene: ftsI, pbpB, PA4418 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 25%(w/v) polyethylene glycol 3350, 0.1M Bis-Tris propane, 1%(w/v) protamine sulphate, pH 7.8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.19→82 Å / Num. obs: 120346 / % possible obs: 100 % / Redundancy: 4.7 % / Rrim(I) all: 0.054 / Net I/σ(I): 14.5
Reflection shellResolution: 1.19→1.21 Å / Rrim(I) all: 0.714

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3oc2

3oc2


Resolution: 1.19→60.08 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.852 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 5816 4.9 %RANDOM
Rwork0.20714 ---
obs0.20807 114094 77.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.014 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2---0.02 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.19→60.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3840 0 0 628 4468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193947
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9695370
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96123.234167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.89515654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7491536
X-RAY DIFFRACTIONr_chiral_restr0.0910.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213013
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: 1.194→1.225 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 69 -
Rwork0.371 1214 -
obs--11.28 %

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