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- PDB-8vbu: Structure of the monofunctional Staphylococcus aureus PBP1 in its... -

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Basic information

Entry
Database: PDB / ID: 8vbu
TitleStructure of the monofunctional Staphylococcus aureus PBP1 in its beta-lactam (Oxacillin) inhibited form
ComponentsPenicillin-binding protein 1
KeywordsHYDROLASE/INHIBITOR / ANTIBIOTIC / Penicillin Binding Protein 1 / Peptidoglycan Transpeptidase domain / Pedestal domain / MEMBRANE PROTEIN / HYDROLASE-INHIBITOR / ANTIBIOTIC complex
Function / homology
Function and homology information


penicillin binding / cell wall organization / plasma membrane
Similarity search - Function
PASTA domain / PASTA domain / PASTA domain profile. / PASTA / 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
Chem-1S6 / Penicillin-binding protein 1
Similarity search - Component
Biological speciesStaphylococcaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBon, C.G. / Lee, J. / Caveney, N.A. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Struct.Biol. / Year: 2024
Title: Structural and kinetic analysis of the monofunctional Staphylococcus aureus PBP1.
Authors: Bon, C.G. / Grigg, J.C. / Lee, J. / Robb, C.S. / Caveney, N.A. / Eltis, L.D. / Strynadka, N.C.J.
History
DepositionDec 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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 1
B: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,0954
Polymers133,2892
Non-polymers8072
Water12,394688
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.949, 72.230, 87.350
Angle α, β, γ (deg.)90.00, 103.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1193-

HOH

21B-1214-

HOH

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Components

#1: Protein Penicillin-binding protein 1


Mass: 66644.258 Da / Num. of mol.: 2 / Fragment: residues 39-608
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcaceae bacterium (bacteria) / Gene: SAOUHSC_01145 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q2FZ94
#2: Chemical ChemComp-1S6 / (2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid / Oxacillin, bound form


Mass: 403.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.18M ammonium citrate 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2→87.55 Å / Num. obs: 73247 / % possible obs: 99.3 % / Redundancy: 2.8 % / CC1/2: 0.726 / Rmerge(I) obs: 0.276 / Rpim(I) all: 0.257 / Net I/σ(I): 3.8
Reflection shellResolution: 2→2.04 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.452 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4466 / CC1/2: 0.339 / Rpim(I) all: 1.337 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→54.97 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 3600 4.97 %
Rwork0.189 --
obs0.1908 72409 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→54.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7754 0 56 688 8498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088006
X-RAY DIFFRACTIONf_angle_d0.90210828
X-RAY DIFFRACTIONf_dihedral_angle_d7.8291129
X-RAY DIFFRACTIONf_chiral_restr0.0551149
X-RAY DIFFRACTIONf_plane_restr0.0071424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.2811460.23032604X-RAY DIFFRACTION97
2.03-2.050.30781450.26062528X-RAY DIFFRACTION95
2.05-2.080.31581330.28682515X-RAY DIFFRACTION95
2.08-2.110.29881480.2252587X-RAY DIFFRACTION96
2.11-2.150.23381250.20132639X-RAY DIFFRACTION98
2.15-2.180.24981430.20332641X-RAY DIFFRACTION98
2.18-2.220.2641300.22522522X-RAY DIFFRACTION95
2.22-2.260.33761300.30912488X-RAY DIFFRACTION92
2.26-2.30.28951310.22772628X-RAY DIFFRACTION97
2.3-2.350.2531480.19952626X-RAY DIFFRACTION98
2.35-2.40.26521230.19242689X-RAY DIFFRACTION99
2.4-2.460.23451350.17462623X-RAY DIFFRACTION99
2.46-2.520.23461460.18452698X-RAY DIFFRACTION100
2.52-2.590.24561410.18222650X-RAY DIFFRACTION99
2.59-2.660.24581170.19092711X-RAY DIFFRACTION99
2.66-2.750.22181390.18792678X-RAY DIFFRACTION99
2.75-2.850.23261360.18952658X-RAY DIFFRACTION99
2.85-2.960.2331420.18422687X-RAY DIFFRACTION100
2.96-3.10.22951680.18242652X-RAY DIFFRACTION100
3.1-3.260.18181290.17182692X-RAY DIFFRACTION100
3.26-3.460.19251410.16482702X-RAY DIFFRACTION99
3.47-3.730.1851370.16482687X-RAY DIFFRACTION99
3.73-4.110.21651370.16312703X-RAY DIFFRACTION99
4.11-4.70.16271420.14872689X-RAY DIFFRACTION99
4.7-5.920.17261410.16442710X-RAY DIFFRACTION99
5.92-54.970.21111470.19532802X-RAY DIFFRACTION100
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)
10.6462-0.4373-0.29190.32490.27320.25530.04270.12640.0507-0.03610.0907-0.1893-0.03270.1659-0.08390.1289-0.02010.0360.1865-0.04380.222335.1012-28.8724-8.0883
20.6668-0.0554-0.00480.56810.07090.9020.0032-0.14030.05790.21-0.0397-0.055-0.0218-0.03580.03640.1753-0.0286-0.01430.113-0.0090.131711.8833-16.716924.668
30.33820.24320.39160.29890.36350.7517-0.0502-0.15430.01460.22490.0849-0.16230.06870.1453-0.01870.19670.0242-0.08750.2131-0.01720.185228.3719-43.714121.9156
40.67410.0172-0.06510.41070.18230.9397-0.00270.119-0.0199-0.08450.0183-0.0516-0.01920.0363-0.00640.0985-0.00730.0070.09240.00770.101820.8332-55.3769-17.7766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 245 )
2X-RAY DIFFRACTION2chain 'A' and (resid 246 through 590 )
3X-RAY DIFFRACTION3chain 'B' and (resid 61 through 245 )
4X-RAY DIFFRACTION4chain 'B' and (resid 246 through 590 )

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