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- PDB-7kcy: Crystal structure of S. aureus penicillin-binding protein 4 (PBP4... -

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Basic information

Entry
Database: PDB / ID: 7kcy
TitleCrystal structure of S. aureus penicillin-binding protein 4 (PBP4) with cefoxitin
ComponentsPenicillin-binding protein 4
KeywordsHYDROLASE/HYDROLASE INHIBITOR / acyl-enzyme intermediate / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase activity / beta-lactam antibiotic catabolic process / peptidoglycan biosynthetic process / cell wall organization / beta-lactamase activity / regulation of cell shape / response to antibiotic / proteolysis / membrane / metal ion binding
Similarity search - Function
Penicillin-binding protein 4, C-terminal domain / Penicillin-binding protein 4, C-terminal domain superfamily / Domain of unknown function (DUF1958) / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-1S7 / Penicillin-binding protein 4
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsAlexander, J.A.N. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Antimicrob.Chemother. / Year: 2021
Title: PBP4-mediated beta-lactam resistance among clinical strains of Staphylococcus aureus.
Authors: Satishkumar, N. / Alexander, J.A.N. / Poon, R. / Buggeln, E. / Argudin, M.A. / Strynadka, N.C.J. / Chatterjee, S.S.
History
DepositionOct 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 9, 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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6244
Polymers41,0981
Non-polymers5263
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.160, 83.010, 103.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Penicillin-binding protein 4


Mass: 41098.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria)
Strain: COL / Gene: pbp4, SACOL0699 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2WY27
#2: Chemical ChemComp-1S7 / (2R)-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / Cefoxitin, bound form


Mass: 368.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16N2O5S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.63 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 12-22% PEG 6000, 100 mM sodium acetate pH 5, and 10 mM zinc acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.5212 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5212 Å / Relative weight: 1
ReflectionResolution: 1.85→45.15 Å / Num. obs: 37412 / % possible obs: 99.2 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.019 / Rrim(I) all: 0.048 / Net I/σ(I): 19.9 / Num. measured all: 237341 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.893.70.836796921340.6560.4780.9691.694.2
9.06-45.155.50.02820973840.9990.0120.03153.398.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.24 Å45.15 Å
Translation6.24 Å45.15 Å

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIXdev 3965refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6c39

6c39


Resolution: 1.85→45.15 Å / SU ML: 0.2194 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.8061
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2146 1961 5.37 %
Rwork0.1886 34525 -
obs0.19 36486 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.14 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2842 0 31 158 3031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672927
X-RAY DIFFRACTIONf_angle_d0.87563966
X-RAY DIFFRACTIONf_chiral_restr0.0479446
X-RAY DIFFRACTIONf_plane_restr0.0058509
X-RAY DIFFRACTIONf_dihedral_angle_d7.1207412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.37141200.33822088X-RAY DIFFRACTION83.95
1.9-1.950.33541300.2942248X-RAY DIFFRACTION89.97
1.95-20.2661350.24312420X-RAY DIFFRACTION95.84
2-2.070.26081360.22442391X-RAY DIFFRACTION95.43
2.07-2.140.26141360.22772394X-RAY DIFFRACTION95.87
2.14-2.230.2571410.21922479X-RAY DIFFRACTION98.42
2.23-2.330.26941440.20992505X-RAY DIFFRACTION98.77
2.33-2.450.22991430.1962517X-RAY DIFFRACTION99.48
2.45-2.610.24891440.19062537X-RAY DIFFRACTION99.67
2.61-2.810.21911440.1982538X-RAY DIFFRACTION99.89
2.81-3.090.25451440.20482556X-RAY DIFFRACTION99.74
3.09-3.540.18611450.18232560X-RAY DIFFRACTION99.38
3.54-4.460.1781460.1472582X-RAY DIFFRACTION99.27
4.46-45.150.18261530.17512710X-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)
11.43083313096-0.5922755649120.08575428349125.177059343791.131777595591.599108089920.0831777323849-0.0362761299690.0162096275417-0.206913544292-0.02856967134470.0511012864442-0.378478425146-0.169237608486-0.06234551668890.2870053619020.04684735645550.03392341578850.2879493475590.009471770814890.1494407379182.005558141429.535471428210.807537292
21.35438798548-0.640255965356-0.3264868162256.262593706251.858098492612.236503306040.116878602913-0.2092279442220.301830487303-0.219209209763-0.0691331647601-0.0391478211302-0.667518081951-0.238686862046-0.05450564183320.4041750327710.05005351611550.0223862851740.323952457586-0.0186607592910.2805713279542.9471039149516.303199194613.8062226084
35.23132058597-1.5188698278-0.9862094177613.235023602930.9795809430981.822266987650.113960407249-0.1816092555760.0671342341681-0.04735977599750.239459928866-0.550300969134-0.1217945855530.249534538907-0.2651738595570.153336859106-0.0332970767153-0.0079141434750.261000940781-0.07615965248460.31954967254617.4061024908-9.862129234446.15618405213
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 23 through 111 )23 - 1111 - 89
22chain 'A' and (resid 112 through 296 )112 - 29690 - 274
33chain 'A' and (resid 297 through 383 )297 - 383275 - 361

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