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

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Basic information

Entry
Database: PDB / ID: 7kcw
TitleCrystal structure of S. aureus penicillin-binding protein 4 (PBP4) mutant (R200L) in complex with nafcillin
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
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-NFF / Penicillin-binding protein 4
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsAlexander, J.A. / Strynadka, N.C.
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

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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)41,7205
Polymers41,0541
Non-polymers6664
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.150, 82.870, 104.630
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: 41054.312 Da / Num. of mol.: 1 / Mutation: R200L
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-NFF / (2R,4S)-2-[(1R)-1-{[(2-ethoxynaphthalen-1-yl)carbonyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / Nafcillin, bound form / Nafcillin


Mass: 416.491 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N2O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 12% PEG 6000; 100 mM sodium acetate, pH 5; and 10 mM zinc chloride

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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: 1.73→42.9 Å / Num. obs: 46311 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.021 / Rrim(I) all: 0.052 / Net I/σ(I): 20.4 / Num. measured all: 282817 / Scaling rejects: 1
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
1.73-1.765.80.6391455524910.8740.2920.7042.499.9
8.99-42.95.60.03422514050.9990.0150.0374599.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.26 Å42.9 Å
Translation6.26 Å42.9 Å

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Processing

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

6c39


Resolution: 1.73→42.9 Å / SU ML: 0.1813 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.06
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2123 1991 4.33 %
Rwork0.1769 44038 -
obs0.1784 46029 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.44 Å2
Refinement stepCycle: LAST / Resolution: 1.73→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 42 315 3187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152926
X-RAY DIFFRACTIONf_angle_d1.32333966
X-RAY DIFFRACTIONf_chiral_restr0.073448
X-RAY DIFFRACTIONf_plane_restr0.0109504
X-RAY DIFFRACTIONf_dihedral_angle_d9.4928419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.32041380.27492970X-RAY DIFFRACTION96.85
1.77-1.820.27771350.24163042X-RAY DIFFRACTION97.75
1.82-1.870.29951400.23433111X-RAY DIFFRACTION99.3
1.87-1.940.31311410.24773118X-RAY DIFFRACTION99.42
1.94-20.23981410.20883128X-RAY DIFFRACTION99.79
2-2.080.2271400.18413109X-RAY DIFFRACTION99.79
2.08-2.180.24661420.19073150X-RAY DIFFRACTION100
2.18-2.290.21871420.18963128X-RAY DIFFRACTION99.85
2.29-2.440.21421420.18673143X-RAY DIFFRACTION99.97
2.44-2.630.20781440.16993168X-RAY DIFFRACTION100
2.63-2.890.22111430.17533169X-RAY DIFFRACTION99.91
2.89-3.310.17561440.17543200X-RAY DIFFRACTION99.97
3.31-4.170.18721470.14843236X-RAY DIFFRACTION99.94
4.17-42.90.19331520.15573366X-RAY DIFFRACTION99.89
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)
13.34056064695-0.14515735561-0.6263072521641.338790138260.3733136297420.838851237880.1614902331990.0135578914714-0.387317775391-0.0669721486680.0878686405056-0.469183229977-0.1099560556010.179982542459-0.1398206849740.126172370472-0.007406865070330.0006085239191850.226218620105-0.1107026340470.40009661030317.2621991629-9.719474844346.10153910009
23.556972214780.02032306143792.606273870317.52208622505-3.500181569347.33576844141-0.123401478348-0.195526436062-0.3677427009230.301429418005-0.1449031451640.300484429330.0538414517204-0.3380686195170.148383079650.125469228674-0.0174202582669-0.02066079490350.224606363912-0.02386457876870.261493962529-9.0314619662-5.9929660524710.9916734959
30.9757709138550.1836592387330.1783586565234.792975966172.204145208571.889919915050.0246713695271-0.03914563199080.102742548225-0.464709136556-0.0123525720504-0.210689446693-0.525756107773-0.0463642306261-0.008724880275880.2676860448440.002912741368740.01837105893680.1786636630050.01509918128880.113839869693.7949199797316.170326221213.1410392147
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 296 through 383 )296 - 383273 - 360
22chain 'A' and (resid 24 through 50 )24 - 501 - 27
33chain 'A' and (resid 51 through 295 )51 - 29528 - 272

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