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- PDB-5ty7: Crystal structure of wild-type S. aureus penicillin binding prote... -

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Basic information

Entry
Database: PDB / ID: 5ty7
TitleCrystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4) in complex with nafcillin
ComponentsPenicillin-binding protein 4
KeywordsHYDROLASE / Antibiotic / HYDROLASE / Antibiotic / HYDROLASE - Antibiotic 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-NFF / Penicillin-binding protein 4
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.894 Å
AuthorsAlexander, J.A.N. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural and kinetic analysis of penicillin-binding protein 4 (PBP4)-mediated antibiotic resistance inStaphylococcus aureus.
Authors: Alexander, J.A.N. / Chatterjee, S.S. / Hamilton, S.M. / Eltis, L.D. / Chambers, H.F. / Strynadka, N.C.J.
History
DepositionNov 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Structure summary
Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.4Oct 23, 2024Group: Refinement description / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 4
B: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,38710
Polymers80,2472
Non-polymers1,1418
Water6,990388
1
A: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7596
Polymers40,1231
Non-polymers6365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6284
Polymers40,1231
Non-polymers5053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.323, 92.231, 79.061
Angle α, β, γ (deg.)90.000, 98.940, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-679-

HOH

DetailsMonomer as determined by size exclusion chromatography

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Components

#1: Protein Penicillin-binding protein 4


Mass: 40123.285 Da / Num. of mol.: 2 / Fragment: residues 25-382
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria)
Strain: COL / Gene: pbp4, SACOL0699 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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


Mass: 416.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24N2O5S / Comment: antibiotic*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 8 mM Zinc chloride, 80 mM sodium acetate pH 5, 400 mM Dimethyl (2-hydroxyethyl) ammonium propane sulfonate, and 16% polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.89→55.59 Å / Num. obs: 63391 / % possible obs: 97.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 25.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.04 / Rrim(I) all: 0.075 / Net I/σ(I): 10.3 / Num. measured all: 203494
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.89-1.943.10.3911178637920.8110.2530.4682.891.1
9.09-55.593.20.02918155640.9980.0190.0352893.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.92 Å46.09 Å
Translation5.92 Å46.09 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
Aimless0.5.28data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TVF

1tvf


Resolution: 1.894→55.588 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 3152 4.98 %
Rwork0.185 60204 -
obs0.1868 63356 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.81 Å2 / Biso mean: 38.2201 Å2 / Biso min: 16.65 Å2
Refinement stepCycle: final / Resolution: 1.894→55.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 64 388 6020
Biso mean--67.86 39.33 -
Num. residues----713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075768
X-RAY DIFFRACTIONf_angle_d0.787838
X-RAY DIFFRACTIONf_chiral_restr0.045888
X-RAY DIFFRACTIONf_plane_restr0.0051006
X-RAY DIFFRACTIONf_dihedral_angle_d11.8783568
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8944-1.92270.42431400.42352309244987
1.9227-1.95270.37961390.33132613275298
1.9527-1.98480.29111490.26462632278198
1.9848-2.0190.28081310.2332594272598
2.019-2.05570.30581400.21782665280598
2.0557-2.09520.30111400.20912593273398
2.0952-2.1380.23261240.20272653277798
2.138-2.18450.23931330.19672617275098
2.1845-2.23530.25371180.22412687280598
2.2353-2.29120.34261360.28982622275898
2.2912-2.35320.26571360.20052630276699
2.3532-2.42240.24181600.18292629278999
2.4224-2.50060.22871400.17852637277799
2.5006-2.590.23821400.18142654279499
2.59-2.69370.24451210.1852649277099
2.6937-2.81630.20691370.17732674281199
2.8163-2.96470.23861260.18292640276698
2.9647-3.15050.23671500.1932610276098
3.1505-3.39370.22611390.17662660279998
3.3937-3.73510.18881310.16212625275698
3.7351-4.27550.15951420.13832611275397
4.2755-5.38590.13961410.13152612275396
5.3859-55.61240.19241390.16872588272794
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)
11.3448-0.8661-1.01182.59481.17542.4736-0.05880.1303-0.05020.11970.05740.16420.0229-0.17330.02190.1814-0.0331-0.02420.19630.01030.180328.8059-47.195841.0984
23.36244.8269-2.01618.7459-1.85351.7848-0.0228-0.0355-0.3684-0.23990.0788-0.58450.16750.0977-0.04040.1617-0.0269-0.00920.3104-0.05380.22234.4452-71.022220.6336
30.3610.73320.83584.83760.40382.3290.01380.07640.0016-0.07420.11490.0333-0.15530.1088-0.14180.2166-0.02880.00560.2743-0.05130.214330.0966-68.308924.1425
43.01661.90961.75698.44912.09794.99640.0916-0.0323-0.33670.5840.0614-0.40140.40450.0105-0.1530.21460.0223-0.05730.2252-0.02590.21938.9167-65.410838.8977
51.7159-0.3555-0.03022.7040.87653.2325-0.04750.2841-0.1813-0.0391-0.00090.40830.1314-0.550.01590.2646-0.0483-0.01930.2896-0.01590.238525.8457-51.337831.6328
64.37311.6288-0.92313.8306-1.05432.35940.11440.34980.5995-0.02880.0041-0.0018-0.30730.1254-0.13080.2587-0.00680.01410.2030.02970.19538.3244-29.77333.7398
70.5742-0.1505-0.4331.82050.16270.8482-0.1383-0.09830.02670.3530.14660.05360.26180.0401-0.00360.32340.056-0.02670.21160.00610.15536.4256-50.6946-3.6034
83.29270.01562.31595.9975-0.36342.36450.0235-0.0742-0.10610.04820.14270.20380.5288-0.2309-0.13240.4472-0.02540.02310.2235-0.01760.142335.9264-65.5962-14.4168
90.7693-0.5221-0.18962.58580.01290.7371-0.1281-0.0432-0.08070.35290.13090.07270.2307-0.0595-0.00230.33340.0325-0.01610.19260.00480.158436.7434-53.7698-5.0711
105.62122.8335-1.17393.1396-0.82531.28990.06710.24810.3940.0880.1094-0.0008-0.01660.1076-0.18870.22040.0497-0.00660.1761-0.02150.181444.8543-27.1783-5.5176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 90 )A25 - 90
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 110 )A91 - 110
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 154 )A111 - 154
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 204 )A155 - 204
5X-RAY DIFFRACTION5chain 'A' and (resid 205 through 296 )A205 - 296
6X-RAY DIFFRACTION6chain 'A' and (resid 297 through 382 )A297 - 382
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 111 )B25 - 111
8X-RAY DIFFRACTION8chain 'B' and (resid 112 through 154 )B112 - 154
9X-RAY DIFFRACTION9chain 'B' and (resid 155 through 296 )B155 - 296
10X-RAY DIFFRACTION10chain 'B' and (resid 297 through 382 )B297 - 382

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