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

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Basic information

Entry
Database: PDB / ID: 8vbw
TitleStructure of the monofunctional Staphylococcus aureus PBP1 in its beta-lactam (Ertapenem) 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-1RG / Penicillin-binding protein 1
Similarity search - Component
Biological speciesStaphylococcaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 23, 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

Downloads & links

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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)134,2444
Polymers133,2892
Non-polymers9552
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.399, 72.717, 90.111
Angle α, β, γ (deg.)90.00, 103.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1052-

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-1RG / (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid / ERTAPENEM, bound form PRE-ISOMERIZED


Mass: 477.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H27N3O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.19 Å3/Da / Density % sol: 43.89 %
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: 2.3→46.03 Å / Num. obs: 51028 / % possible obs: 99.1 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.062 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 4.1 % / Rmerge(I) obs: 2.687 / Num. unique obs: 4391 / CC1/2: 0.429 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.03 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 2449 4.84 %
Rwork0.1925 --
obs0.1945 50582 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7746 0 66 314 8126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087984
X-RAY DIFFRACTIONf_angle_d0.90910796
X-RAY DIFFRACTIONf_dihedral_angle_d7.511127
X-RAY DIFFRACTIONf_chiral_restr0.0531150
X-RAY DIFFRACTIONf_plane_restr0.0071422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.71341280.76882407X-RAY DIFFRACTION84
2.35-2.40.43591360.44822839X-RAY DIFFRACTION99
2.4-2.450.35571480.31852828X-RAY DIFFRACTION99
2.45-2.520.35671610.26492845X-RAY DIFFRACTION99
2.52-2.580.29991400.23222805X-RAY DIFFRACTION99
2.58-2.660.24741410.22852828X-RAY DIFFRACTION99
2.66-2.740.26511430.22732823X-RAY DIFFRACTION98
2.75-2.840.28671380.23672834X-RAY DIFFRACTION100
2.84-2.960.30111500.26142878X-RAY DIFFRACTION100
2.96-3.090.29661250.23082901X-RAY DIFFRACTION100
3.09-3.250.24831570.19742841X-RAY DIFFRACTION100
3.25-3.460.26211520.1932847X-RAY DIFFRACTION99
3.46-3.730.22021300.18312851X-RAY DIFFRACTION98
3.73-4.10.19561450.15142852X-RAY DIFFRACTION98
4.1-4.690.16571430.12392883X-RAY DIFFRACTION100
4.69-5.910.14771580.13722903X-RAY DIFFRACTION100
5.91-46.030.18821540.16132968X-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)
11.8449-0.8358-0.53090.7920.84841.21620.05690.03070.1262-0.42920.4688-0.6425-0.21120.6735-0.42070.3923-0.10250.14690.6158-0.1820.706441.1144-29.3-10.8493
20.8201-0.1688-0.31440.7320.19671.5817-0.0586-0.11190.04640.14980.0055-0.0566-0.0322-0.06840.05080.3339-0.0024-0.06580.27420.00190.294310.4238-19.830720.1421
31.5099-0.3202-0.42941.1530.02092.554-0.0065-0.17870.02710.32870.0569-0.0219-0.1520.2038-0.01890.3781-0.0077-0.12640.332-0.02790.374719.6956-12.398726.9915
41.74080.82711.43491.0281.39412.6662-0.1346-0.182-0.08330.25570.3087-0.1988-0.05020.6274-0.17710.48430.0228-0.09060.60590.00130.377732.7599-43.175827.4336
50.51720.38490.76630.64561.1162.1077-0.0103-0.1788-0.03910.2630.1408-0.34730.05350.3061-0.15120.53250.051-0.12550.52070.02560.462831.7249-44.658324.1826
61.2371.36460.92423.58820.65971.47090.0961-0.248-0.00540.3503-0.15540.2020.1885-0.13620.04410.33890.02350.00770.3650.01550.373915.4446-45.293211.4098
71.67580.43590.10241.20090.20161.673-0.19820.3499-0.1812-0.32580.1328-0.183-0.00910.0370.05230.3806-0.04070.09890.3308-0.04690.353620.9959-51.891-20.8488
81.41360.051-0.57960.78020.33981.9275-0.1630.1845-0.2697-0.13630.0696-0.19930.10350.08670.0840.3301-0.02820.06370.3071-0.04550.404417.4616-59.2629-14.8912
92.98741.2605-0.98352.4055-1.03232.97-0.19230.064-0.5684-0.38020.0667-0.58320.51180.44780.08970.36840.04090.08340.3707-0.10940.580230.5872-61.8857-12.2641
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 494 )
3X-RAY DIFFRACTION3chain 'A' and (resid 495 through 590 )
4X-RAY DIFFRACTION4chain 'B' and (resid 61 through 129 )
5X-RAY DIFFRACTION5chain 'B' and (resid 130 through 182 )
6X-RAY DIFFRACTION6chain 'B' and (resid 183 through 245 )
7X-RAY DIFFRACTION7chain 'B' and (resid 246 through 430 )
8X-RAY DIFFRACTION8chain 'B' and (resid 431 through 548 )
9X-RAY DIFFRACTION9chain 'B' and (resid 549 through 590 )

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