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- PDB-8c5b: Crystal Structure of Penicillin-binding Protein 3 (PBP3) from Sta... -

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Basic information

Entry
Database: PDB / ID: 8c5b
TitleCrystal Structure of Penicillin-binding Protein 3 (PBP3) from Staphylococcus Epidermidis
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
Penicillin-binding protein 3
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 3


Theoretical massNumber of molelcules
Total (without water)74,9321
Polymers74,9321
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area29110 Å2
Unit cell
Length a, b, c (Å)83.442, 83.442, 307.155
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

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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: 3.57 Å3/Da / Density % sol: 65.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate

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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: 0.97625 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: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.067→80.687 Å / Num. obs: 46353 / % possible obs: 95.2 % / Redundancy: 18.8 % / Biso Wilson estimate: 56.24 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.8
Reflection shellResolution: 2.067→2.297 Å / Num. unique obs: 2318 / CC1/2: 0.996

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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: 2.5→57.94 Å / SU ML: 0.3166 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.7949
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2565 1762 4.95 %
Rwork0.2211 33834 -
obs0.2229 35596 91.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.95 Å2
Refinement stepCycle: LAST / Resolution: 2.5→57.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4870 0 0 0 4870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00844949
X-RAY DIFFRACTIONf_angle_d1.04876687
X-RAY DIFFRACTIONf_chiral_restr0.0529746
X-RAY DIFFRACTIONf_plane_restr0.0082877
X-RAY DIFFRACTIONf_dihedral_angle_d6.8934680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.4426620.32131285X-RAY DIFFRACTION45.79
2.57-2.640.3794800.29311654X-RAY DIFFRACTION60.02
2.64-2.730.2921300.27382396X-RAY DIFFRACTION86.45
2.73-2.830.31041580.28582755X-RAY DIFFRACTION99.52
2.83-2.940.35821370.31022783X-RAY DIFFRACTION99.97
2.94-3.070.31941750.28292777X-RAY DIFFRACTION99.97
3.07-3.230.29171270.25772807X-RAY DIFFRACTION100
3.23-3.440.30531460.25892799X-RAY DIFFRACTION99.93
3.44-3.70.25621420.23942840X-RAY DIFFRACTION99.97
3.7-4.080.23891510.20552840X-RAY DIFFRACTION100
4.08-4.660.23781320.18252897X-RAY DIFFRACTION100
4.67-5.880.2331530.18922904X-RAY DIFFRACTION100
5.88-57.940.20191690.18933097X-RAY DIFFRACTION99.94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.515636612976-0.3813491504190.39602186669-0.1605992785860.2712039161540.538343701241-0.08195243625370.047718486052-0.0934260391922-0.07148695865960.1046306080480.118097909439-0.105174898353-0.0399713584956-0.005945342991630.37959547828-0.116227748997-0.04022181475990.817008464950.03260106450320.450469901014-14.8959545337-12.5632821835-75.1410379783
21.221942160730.348606408574-0.5841329728880.663063252601-0.3260506038141.107697344420.04050642996020.036014087947-0.05443321529030.06612104069360.00359924733233-0.00513625342167-0.00608206072368-0.07427057922221.15251356072E-50.1778969017720.0556931370135-0.005729462460790.365754303723-0.07872222280760.27707704743-16.2501912674-20.4575745788-25.7578622713
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 48 through 341 )48 - 3411 - 294
22chain 'A' and (resid 342 through 679 )342 - 679295 - 632

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