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- PDB-8c5w: Crystal Structure of Penicillin-binding Protein 3 (PBP3) from Sta... -

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Basic information

Entry
Database: PDB / ID: 8c5w
TitleCrystal Structure of Penicillin-binding Protein 3 (PBP3) from Staphylococcus Epidermidis in complex with Cefotaxime
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
CEFOTAXIME, C3' cleaved, open, bound form / Penicillin-binding protein 3
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 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 13, 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)75,3292
Polymers74,9321
Non-polymers3971
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-1 kcal/mol
Surface area30390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.061, 83.061, 308.864
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) (bacteria)
Gene: pbp3, SERP1117 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5HNZ7
#2: Chemical ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form


Mass: 397.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.55 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate + Cefotaxime

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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: 1.03321 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.5→49.236 Å / Num. obs: 70884 / % possible obs: 99.9 % / Redundancy: 13.7 % / Biso Wilson estimate: 90.32 Å2 / CC1/2: 0.999 / Net I/σ(I): 0.99
Reflection shellResolution: 2.5→2.512 Å / Num. unique obs: 11304 / CC1/2: 0.956

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→46.75 Å / SU ML: 0.5099 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.0848
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2532 3542 5.49 %
Rwork0.2313 60948 -
obs0.2325 64490 90.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.21 Å2
Refinement stepCycle: LAST / Resolution: 2.51→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4944 0 26 5 4975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01815049
X-RAY DIFFRACTIONf_angle_d1.64056809
X-RAY DIFFRACTIONf_chiral_restr0.0705751
X-RAY DIFFRACTIONf_plane_restr0.0168891
X-RAY DIFFRACTIONf_dihedral_angle_d9.8756691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.540.388230.4208437X-RAY DIFFRACTION16.35
2.54-2.580.4647610.3951145X-RAY DIFFRACTION42.38
2.58-2.610.396990.39331730X-RAY DIFFRACTION64.63
2.61-2.660.37181040.37431833X-RAY DIFFRACTION68.54
2.66-2.70.41011340.37672331X-RAY DIFFRACTION87.19
2.7-2.750.33641530.38352606X-RAY DIFFRACTION96.91
2.75-2.80.35861540.37952675X-RAY DIFFRACTION99.3
2.8-2.850.45851520.4262685X-RAY DIFFRACTION99.89
2.85-2.910.42451560.41062660X-RAY DIFFRACTION99.82
2.91-2.970.46281560.38712674X-RAY DIFFRACTION99.96
2.97-3.040.44591560.3762648X-RAY DIFFRACTION99.86
3.04-3.120.37671620.34072700X-RAY DIFFRACTION100
3.12-3.20.37081580.31532701X-RAY DIFFRACTION100
3.2-3.290.29661600.29492658X-RAY DIFFRACTION100
3.29-3.40.31181550.29432664X-RAY DIFFRACTION99.96
3.4-3.520.33361540.23862688X-RAY DIFFRACTION100
3.52-3.660.26511500.22452685X-RAY DIFFRACTION100
3.66-3.830.23881620.20922672X-RAY DIFFRACTION100
3.83-4.030.26421590.20862684X-RAY DIFFRACTION99.96
4.03-4.280.22911530.19742670X-RAY DIFFRACTION99.93
4.28-4.610.22621530.19912723X-RAY DIFFRACTION99.93
4.61-5.080.20821600.20262643X-RAY DIFFRACTION99.79
5.08-5.810.25261570.21282687X-RAY DIFFRACTION100
5.81-7.320.26141550.22732675X-RAY DIFFRACTION100
7.32-46.750.16451560.18022674X-RAY DIFFRACTION99.72

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