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

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Basic information

Entry
Database: PDB / ID: 7kcx
TitleCrystal structure of S. aureus penicillin-binding protein 4 (PBP4) mutant (R200L) in complex 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 / metal ion binding / membrane
Similarity search - Function
Penicillin-binding protein 4, C-terminal domain / 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 / Spermidine Synthase; Chain: A, domain 2 / Beta-lactamase, class-A ...Penicillin-binding protein 4, C-terminal domain / 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 / Spermidine Synthase; Chain: A, domain 2 / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
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: 1.62 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 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

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Assembly

Deposited unit
A: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6725
Polymers41,0541
Non-polymers6184
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.080, 82.700, 103.860
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-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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.62 Å3/Da / Density % sol: 53.04 %
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: 1.62→45.11 Å / Num. obs: 52537 / % possible obs: 94.8 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Net I/σ(I): 22.4 / Num. measured all: 341149 / Scaling rejects: 3
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
1.62-1.656.31.481522424050.6290.6261.6111.189.4
8.87-45.115.40.03421794000.9990.0150.03759.398.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.23 Å43.98 Å
Translation6.23 Å43.98 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: 1.62→43.98 Å / SU ML: 0.2068 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.1999
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2043 1959 3.81 %
Rwork0.1756 49446 -
obs0.1767 51405 92.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.52 Å2
Refinement stepCycle: LAST / Resolution: 1.62→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2839 0 37 242 3118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01052947
X-RAY DIFFRACTIONf_angle_d1.17783995
X-RAY DIFFRACTIONf_chiral_restr0.0649450
X-RAY DIFFRACTIONf_plane_restr0.01511
X-RAY DIFFRACTIONf_dihedral_angle_d8.0899419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.41461210.34893019X-RAY DIFFRACTION80.78
1.66-1.710.27711280.28713163X-RAY DIFFRACTION84.23
1.71-1.760.33231280.24913283X-RAY DIFFRACTION86.73
1.76-1.810.28261220.26543165X-RAY DIFFRACTION84.28
1.81-1.880.31411380.2513476X-RAY DIFFRACTION91.59
1.88-1.950.27471410.20883523X-RAY DIFFRACTION93.23
1.95-2.040.21981400.18363543X-RAY DIFFRACTION93.74
2.04-2.150.20381450.17763632X-RAY DIFFRACTION95.14
2.15-2.280.21841440.18033651X-RAY DIFFRACTION95.69
2.28-2.460.18291460.16373660X-RAY DIFFRACTION96.26
2.46-2.710.19171470.16563713X-RAY DIFFRACTION97.11
2.71-3.10.21561500.17273779X-RAY DIFFRACTION97.57
3.1-3.90.19671510.16093825X-RAY DIFFRACTION98.25
3.9-43.980.16431580.15554014X-RAY DIFFRACTION98.65
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)
12.06771377468-0.490309505028-1.236540368125.21515819780.8869836448884.51688715604-0.0712675506159-0.0101069276444-0.6263099354550.0881786190245-0.2487781349260.482188555541-0.070801594084-0.3154775742410.2650237025460.164603348152-0.0183894263819-0.03812451733390.326347888424-0.008216741773660.369724033495-8.60150500692-5.7678660837410.0476219082
20.5924728768160.09242111682330.2451337183994.271850199541.511073507271.308005596290.04337622475270.005431226319610.098063015786-0.4238340278240.0142375340737-0.322430763003-0.467285218068-0.0127864488932-0.06878720940090.3346199966930.0006684162763010.05490014427850.2527961364060.005485742812360.1934956077236.3435803995815.924247923411.1806350641
31.244617612970.0579919451070.7229889808834.00757960521.068092024812.66654600647-0.0460286365965-0.1047771206240.339010329037-0.775971774718-0.0824279491581-0.257568860376-0.801612094025-0.159886483929-0.05475617144440.6012967700860.04123941835450.04913233704980.197292770975-0.003228054088680.2112414984893.6650488821924.421624734811.9101215875
41.373619537830.108810836279-0.1562650179334.530795722161.737969853622.637078469260.0879871619075-0.100490583770.0792784199478-0.062486857037-0.07356961717780.0383173622158-0.381262268558-0.18017762985-0.02375394866960.2088772176850.02675666299080.004295559648560.2199767615170.009634470088060.1464111527952.2310244808210.244451286915.163954673
52.47315425608-0.255631128762-0.8396776647271.663615284880.7098385963011.562723837330.0942129988742-0.325692734996-0.01293357142670.0889662683570.204667857792-0.376935435551-0.005124766899910.205851299414-0.2078131452060.140471132369-0.0153810397567-0.03799558352930.241329081491-0.02913811758570.28043701185913.3152403621-9.2540678709511.0050666396
64.739849123330.227574920145-0.5907710114471.758999319640.5443317536851.570419813420.1265540310810.1468584796070.0221219437822-0.1167168750220.271271406811-0.635264529379-0.03469078744630.215922022737-0.213974774470.1670846280550.005375798773030.02401559309020.289026623597-0.1251794350710.49495917471620.8424385427-13.24716020483.54826875711
73.34879330409-0.920015312225-0.9424957270940.816078860.4341507157920.8206515116710.369990042680.350781933303-0.160303772556-0.558176880090.0153618947363-1.10285175043-0.3367308459560.267245681103-0.2417152421530.187231953807-0.02404583023970.1388058617820.290792234733-0.09158890364040.49848539416819.3549055525-5.366828196830.0780059558958
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 50 )23 - 501 - 28
22chain 'A' and (resid 51 through 111 )51 - 11129 - 89
33chain 'A' and (resid 112 through 190 )112 - 19090 - 168
44chain 'A' and (resid 191 through 295 )191 - 295169 - 273
55chain 'A' and (resid 296 through 335 )296 - 335274 - 313
66chain 'A' and (resid 336 through 364 )336 - 364314 - 342
77chain 'A' and (resid 365 through 383 )365 - 383343 - 361

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