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- PDB-8c5o: Crystal Structure of Penicillin-binding Protein 3 (PBP3) from Sta... -

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Basic information

Entry
Database: PDB / ID: 8c5o
TitleCrystal Structure of Penicillin-binding Protein 3 (PBP3) from Staphylococcus Epidermidis in complex with Vaborbactam
ComponentsPenicillin-binding protein 3
KeywordsPENICILLIN-BINDING PROTEIN
Function / homology
Function and homology information


peptidoglycan L,D-transpeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / plasma membrane
Similarity search - Function
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/transpeptidase-like
Similarity search - Domain/homology
Vaborbactam / Penicillin-binding protein 3
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSchwinzer, M. / Brognaro, H. / Rohde, H. / Betzel, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Int J Appl Biol Pharm / Year: 2023
Title: Structure and Dynamics of the Penicillin-Binding Protein 3 from Staphylococcus Epidermidis Native and in Complex with Cefotaxime and Vaborbactam
Authors: Schwinzer, M. / Brognaro, H. / Rohde, H. / Betzel, C.
History
DepositionJan 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_id_ISSN / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2292
Polymers74,9321
Non-polymers2971
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area28640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.152, 83.152, 306.136
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Penicillin-binding protein 3


Mass: 74932.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (strain ATCC 35984 / RP62A)
Gene: pbp3, SERP1117 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5HNZ7
#2: Chemical ChemComp-4D6 / Vaborbactam / {(3R,6S)-2-hydroxy-3-[(thiophen-2-ylacetyl)amino]-1,2-oxaborinan-6-yl}acetic acid / 2-((3R,6S)-2-hydroxy-3-(2-(thiophen-2-yl)acetamido)-1,2-oxaborinan-6-yl)acetic acid / 2-[(3R,6S)-2-hydroxy-3-[(2-thiophen-2-ylacetyl)amino]oxaborinan-6-yl]acetic acid / 1,2-Oxaborinane-6-acetic acid, 2-hydroxy-3-((2-(2-thienyl)acetyl)amino)-, (3R,6S)-


Mass: 297.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16BNO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.53 Å3/Da / Density % sol: 65.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate + Vaborbactam

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.82655 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82655 Å / Relative weight: 1
ReflectionResolution: 2.3→80.245 Å / Num. obs: 50577 / % possible obs: 92.6 % / Redundancy: 18.2 % / Biso Wilson estimate: 36.29 Å2 / CC1/2: 0.9642 / Net I/σ(I): 3.988
Reflection shellResolution: 2.309→2.364 Å / Num. unique obs: 3160 / CC1/2: 0.9642

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Processing

Software
NameVersionClassification
PHENIXv1.19.2-4158refinement
PHENIXv1.19.2-4158refinement
XDSdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50.95 Å / SU ML: 0.2548 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.1967
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2272 2414 5.03 %
Rwork0.199 45592 -
obs0.2004 48006 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.9 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4870 0 20 338 5228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794970
X-RAY DIFFRACTIONf_angle_d0.99546715
X-RAY DIFFRACTIONf_chiral_restr0.0531748
X-RAY DIFFRACTIONf_plane_restr0.0075880
X-RAY DIFFRACTIONf_dihedral_angle_d10.8016689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.29741190.23862661X-RAY DIFFRACTION98.76
2.35-2.40.2651490.23542662X-RAY DIFFRACTION100
2.4-2.450.25461550.21972689X-RAY DIFFRACTION100
2.45-2.520.2531490.21292664X-RAY DIFFRACTION100
2.52-2.580.23261390.20372695X-RAY DIFFRACTION99.96
2.58-2.660.24061520.20172670X-RAY DIFFRACTION100
2.66-2.740.25181210.2032338X-RAY DIFFRACTION87.14
2.75-2.840.23581450.21432704X-RAY DIFFRACTION100
2.84-2.960.25611480.2372733X-RAY DIFFRACTION100
2.96-3.090.2781260.22992735X-RAY DIFFRACTION99.97
3.09-3.250.26061360.21522704X-RAY DIFFRACTION100
3.25-3.460.25321380.21042599X-RAY DIFFRACTION94.54
3.46-3.720.23621480.20142505X-RAY DIFFRACTION92.6
3.73-4.10.2191390.17442583X-RAY DIFFRACTION93.77
4.1-4.690.17661420.16032801X-RAY DIFFRACTION100
4.69-5.910.20961500.18142836X-RAY DIFFRACTION100
5.91-50.950.19271580.20083013X-RAY DIFFRACTION99.78

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