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

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Basic information

Entry
Database: PDB / ID: 8vbv
TitleStructure of the monofunctional Staphylococcus aureus PBP1 in its beta-lactam (Cephalexin) 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-63U / Penicillin-binding protein 1
Similarity search - Component
Biological speciesStaphylococcaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 30, 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)133,9874
Polymers133,2892
Non-polymers6992
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.076, 72.531, 89.595
Angle α, β, γ (deg.)90.00, 103.85, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-989-

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-63U / (2S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid


Mass: 349.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
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: CLSI / Beamline: 08B1-1 / Wavelength: 1.5211 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5211 Å / Relative weight: 1
ReflectionResolution: 2.4→45.74 Å / Num. obs: 43743 / % possible obs: 98.2 % / Redundancy: 3.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.062 / Net I/σ(I): 6.2
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 1.314 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4565 / CC1/2: 0.581 / Rpim(I) all: 1.204

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.74 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 2104 4.83 %
Rwork0.2014 --
obs0.2032 43578 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7752 0 48 169 7969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087982
X-RAY DIFFRACTIONf_angle_d1.00710786
X-RAY DIFFRACTIONf_dihedral_angle_d6.9691115
X-RAY DIFFRACTIONf_chiral_restr0.0641143
X-RAY DIFFRACTIONf_plane_restr0.0081423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.64871090.70532627X-RAY DIFFRACTION93
2.46-2.520.51371460.48192744X-RAY DIFFRACTION98
2.52-2.590.43721390.36132785X-RAY DIFFRACTION98
2.59-2.660.32261460.2962730X-RAY DIFFRACTION98
2.66-2.750.36391240.2792732X-RAY DIFFRACTION97
2.75-2.850.35361540.29462737X-RAY DIFFRACTION97
2.85-2.960.37991330.3252723X-RAY DIFFRACTION97
2.96-3.090.27681250.25062777X-RAY DIFFRACTION97
3.09-3.260.24591210.22462736X-RAY DIFFRACTION97
3.26-3.460.26951520.20852758X-RAY DIFFRACTION98
3.46-3.730.24381580.17942749X-RAY DIFFRACTION98
3.73-4.10.18371470.15022815X-RAY DIFFRACTION99
4.1-4.70.1811440.12722833X-RAY DIFFRACTION100
4.7-5.910.16251560.13842827X-RAY DIFFRACTION99
5.92-45.740.1741500.16962901X-RAY DIFFRACTION99
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)
12.4111-0.8825-0.51981.60361.40791.67320.1950.11990.1336-0.340.4361-0.8856-0.12740.5194-0.61120.4715-0.08750.11880.5758-0.14380.817441.0591-29.3195-10.3016
21.0526-0.3045-0.34920.8510.27661.4071-0.0496-0.14710.06670.13340.0251-0.0211-0.0328-0.04530.03130.46810.0011-0.04150.4126-0.00430.422511.2672-20.989921.1966
30.82530.0415-0.32790.7890.44081.65060.0534-0.23050.12840.1174-0.0148-0.1659-0.14180.0183-0.02670.47560.0157-0.05920.3841-0.01790.475514.7221-12.134323.3373
41.34040.02210.70811.44961.15942.6522-0.0052-0.2622-0.01040.32810.064-0.19160.12360.2957-0.05760.47720.0075-0.04390.49590.03320.466628.1757-44.024222.5298
51.33180.29930.23340.90530.2621.9358-0.05690.2665-0.0773-0.21260.0271-0.1592-0.0540.04240.02820.4318-0.00520.06490.4235-0.02870.478721.0255-51.7999-20.7827
60.8672-0.1099-0.220.84810.74051.8084-0.03020.1447-0.1116-0.02690.0824-0.1510.08920.0918-0.04820.4160.01270.01630.3803-0.02720.492321.1069-59.6247-14.2985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 177 )
2X-RAY DIFFRACTION2chain 'A' and (resid 178 through 457 )
3X-RAY DIFFRACTION3chain 'A' and (resid 458 through 589 )
4X-RAY DIFFRACTION4chain 'B' and (resid 61 through 245 )
5X-RAY DIFFRACTION5chain 'B' and (resid 246 through 430 )
6X-RAY DIFFRACTION6chain 'B' and (resid 431 through 589 )

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