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- PDB-8f67: Crystal structure of the refolded Penicillin Binding Protein 5 (P... -

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Basic information

Entry
Database: PDB / ID: 8f67
TitleCrystal structure of the refolded Penicillin Binding Protein 5 (PBP5) of Enterococcus faecium
ComponentsPbp5Muramoylpentapeptide carboxypeptidase
KeywordsANTIBIOTIC / Penicillin binding / antibiotic resistance / antibiotics
Function / homology
Function and homology information


penicillin binding / response to antibiotic / plasma membrane
Similarity search - Function
NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / 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 / NTF2-like domain superfamily / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsD'Andrea, E.D. / Schoenle, M.V. / Choy, M.S. / Peti, W. / Page, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2023
Title: The Molecular Basis for Resistance of E. faecium PBP5 to beta-lactam Antibiotics
Authors: Hunashal, Y. / Kumar, G.S. / Choy, M.S. / Da Silva Santiago, A. / D'Andrea, E.D. / Schoenle, M.V. / Arthur, M. / Rice, L.B. / Page, R. / Peti, W.
History
DepositionNov 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: 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: Pbp5
B: Pbp5
C: Pbp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,91769
Polymers209,5763
Non-polymers6,34066
Water2,306128
1
A: Pbp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,87622
Polymers69,8591
Non-polymers2,01721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pbp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,97223
Polymers69,8591
Non-polymers2,11322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Pbp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,06824
Polymers69,8591
Non-polymers2,20923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)190.937, 331.666, 156.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Pbp5 / Muramoylpentapeptide carboxypeptidase


Mass: 69858.781 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: pbp5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A075Q0W3
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 66 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 5.9 Å3/Da / Density % sol: 79.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES pH 6.0, 3.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.59→39.63 Å / Num. obs: 57949 / % possible obs: 99.3 % / Redundancy: 6.8 % / CC1/2: 0.977 / Rmerge(I) obs: 0.293 / Rpim(I) all: 0.121 / Rrim(I) all: 0.317 / Χ2: 0.97 / Net I/σ(I): 8 / Num. measured all: 393565
Reflection shellResolution: 3.59→3.68 Å / % possible obs: 92.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 1.096 / Num. measured all: 26257 / Num. unique obs: 4185 / CC1/2: 0.605 / Rpim(I) all: 0.47 / Rrim(I) all: 1.197 / Χ2: 1.01 / Net I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MKA

6mka


Resolution: 3.59→39.63 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2138 2905 5.04 %
Rwork0.1796 --
obs0.1813 57654 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.59→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14222 0 330 128 14680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214708
X-RAY DIFFRACTIONf_angle_d0.4320022
X-RAY DIFFRACTIONf_dihedral_angle_d12.4865203
X-RAY DIFFRACTIONf_chiral_restr0.042273
X-RAY DIFFRACTIONf_plane_restr0.0032594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.59-3.650.26031250.23242192X-RAY DIFFRACTION86
3.65-3.710.23981280.21972592X-RAY DIFFRACTION100
3.71-3.780.23661480.20272607X-RAY DIFFRACTION100
3.78-3.850.25191340.21152601X-RAY DIFFRACTION100
3.85-3.930.24061260.19632626X-RAY DIFFRACTION100
3.93-4.010.23221430.18562590X-RAY DIFFRACTION100
4.01-4.110.22421480.17782589X-RAY DIFFRACTION99
4.11-4.210.20861390.1632611X-RAY DIFFRACTION100
4.21-4.320.21531410.15582608X-RAY DIFFRACTION100
4.32-4.450.21761320.15642611X-RAY DIFFRACTION100
4.45-4.590.19111230.15732637X-RAY DIFFRACTION100
4.59-4.760.20471470.15512618X-RAY DIFFRACTION100
4.76-4.950.18041190.15932640X-RAY DIFFRACTION100
4.95-5.170.20111430.16642635X-RAY DIFFRACTION100
5.17-5.440.211600.1672586X-RAY DIFFRACTION100
5.44-5.780.21481400.19182635X-RAY DIFFRACTION100
5.78-6.230.2371350.20262629X-RAY DIFFRACTION100
6.23-6.850.22611560.18762640X-RAY DIFFRACTION100
6.85-7.840.21651480.19342645X-RAY DIFFRACTION100
7.84-9.850.16991470.15532715X-RAY DIFFRACTION100
9.85-39.630.20361230.20112742X-RAY DIFFRACTION98

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