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- PDB-5tx9: Crystal structure of S. aureus penicillin binding protein 4 (PBP4... -

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Basic information

Entry
Database: PDB / ID: 5tx9
TitleCrystal structure of S. aureus penicillin binding protein 4 (PBP4) mutant (E183A, F241R) in complex with ceftobiprole
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 / 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-RB6 / Penicillin-binding protein 4
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 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 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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

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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)81,83412
Polymers80,4072
Non-polymers1,42710
Water12,809711
1
A: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9176
Polymers40,2031
Non-polymers7135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9176
Polymers40,2031
Non-polymers7135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.882, 92.252, 79.381
Angle α, β, γ (deg.)90.000, 100.220, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-402-

ZN

21A-791-

HOH

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Components

#1: Protein Penicillin-binding protein 4


Mass: 40203.398 Da / Num. of mol.: 2 / Fragment: residues 25-383 / Mutation: E183A, F241R
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-RB6 / (2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / BAL 9141, bound form / ceftobiprole, bound form


Mass: 536.585 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N8O6S2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 711 / Source method: isolated from a natural source / Formula: H2O

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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: 296 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 8 mM Zinc chloride, 80 mM sodium acetate pH 5, 100 mM sodium fluoride, 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: 1.68→32.84 Å / Num. obs: 93450 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.049 / Rrim(I) all: 0.095 / Net I/σ(I): 9.6 / Num. measured all: 346737
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.68-1.713.80.7950.736199.9
9.2-32.843.60.0290.999197.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.86 Å46.1 Å
Translation5.86 Å46.1 Å

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Processing

Software
NameVersionClassification
Aimless0.5.28data scaling
PHASER2.5.6phasing
PHENIX(1.11.1_2575)refinement
XDSdata reduction
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TVF

1tvf


Resolution: 1.68→32.837 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.13
RfactorNum. reflection% reflection
Rfree0.2411 4638 5.03 %
Rwork0.2078 --
obs0.2095 92227 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.54 Å2 / Biso mean: 22.3395 Å2 / Biso min: 9.05 Å2
Refinement stepCycle: final / Resolution: 1.68→32.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5601 0 80 711 6392
Biso mean--24.01 32.44 -
Num. residues----717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075810
X-RAY DIFFRACTIONf_angle_d0.9637888
X-RAY DIFFRACTIONf_chiral_restr0.052891
X-RAY DIFFRACTIONf_plane_restr0.0061021
X-RAY DIFFRACTIONf_dihedral_angle_d11.8873624
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.68-1.69910.28361680.281529623130100
1.6991-1.71910.30181570.29129563113100
1.7191-1.740.33921500.27242972312299
1.74-1.76210.27511850.258229793164100
1.7621-1.78530.28521510.247129173068100
1.7853-1.80970.28251650.233729903155100
1.8097-1.83560.24191560.226129673123100
1.8356-1.8630.25341480.224729653113100
1.863-1.89210.31181580.28342955311399
1.8921-1.92310.6041730.56412539271287
1.9231-1.95620.46011470.36462610275787
1.9562-1.99180.25191470.222829503097100
1.9918-2.03010.20351620.195630013163100
2.0301-2.07150.32361390.28882838297795
2.0715-2.11660.30741470.24542876302397
2.1166-2.16580.21491380.179329783116100
2.1658-2.220.23031560.179229713127100
2.22-2.280.45571080.36112482259081
2.28-2.3470.23711540.19792950310499
2.347-2.42280.20541620.172529723134100
2.4228-2.50930.18861670.17472941310899
2.5093-2.60980.2581430.17832963310699
2.6098-2.72850.22831550.18842978313399
2.7285-2.87230.23521440.175530033147100
2.8723-3.05210.21081610.168429873148100
3.0521-3.28750.19291520.16962955310799
3.2875-3.6180.21431540.17152952310698
3.618-4.14070.17821640.16222936310098
4.1407-5.21340.15451600.140130013161100
5.2134-32.84320.17131670.17963043321099
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)
10.7046-0.4974-0.5581.44090.39471.0899-0.0250.0679-0.02570.03810.02760.0789-0.0164-0.0445-0.00680.1044-0.0216-0.02760.1431-0.00430.11528.5535-48.029740.8059
21.09811.38290.59985.34090.03881.90130.0428-0.0489-0.03050.0794-0.01710.0142-0.07890.0146-0.04560.1348-0.0017-0.01360.1607-0.01930.094529.6161-70.251122.3819
32.17621.17071.0034.53461.23783.13730.0160.0268-0.11230.0830.0624-0.17490.2825-0.0138-0.09840.1150.0188-0.02880.1203-0.02130.115137.8224-66.63136.455
41.0762-0.4327-0.10541.5919-0.10881.0571-0.00960.1412-0.0485-0.0875-0.00080.12370.0759-0.15780.01520.1144-0.0291-0.01870.1498-0.02610.110525.7665-52.02431.682
53.95611.8892-0.79152.9728-0.9841.31420.01280.25040.4177-0.0427-0.0015-0.003-0.08280.0674-0.00720.12990.0183-0.0150.14780.00680.107838.612-30.434133.4494
60.9986-0.454-0.85961.93510.52581.6906-0.0242-0.05450.02710.26370.03540.14130.0211-0.0175-0.00950.11-0.0075-0.0160.11390.00830.07535.6034-45.20641.4455
71.28281.433-0.07355.6881-1.52032.5733-0.0776-0.0704-0.134-0.10620.05340.08980.3238-0.13390.00990.18120.0048-0.00430.1431-0.02050.10938.0981-67.1562-15.6291
82.01321.6099-0.01088.11770.84212.43590.0305-0.1018-0.10010.374-0.107-0.13270.1867-0.01030.08340.14190.0195-0.04040.12110.02620.082645.9223-63.0777-0.2578
91.02550.29590.04821.18950.13940.67350.00260.05640.08680.02680.0030.0750.0066-0.0062-0.00430.11220.0079-0.00310.13750.01680.110737.6206-39.3176-7.1079
103.67842.2904-0.98877.3317-1.56744.2975-0.06620.1907-0.1783-0.1229-0.0398-0.43910.09910.23060.17510.0636-0.0096-0.03720.1417-0.00860.174852.6531-31.0789-3.9434
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 137 )A91 - 137
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 204 )A138 - 204
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 296 )A205 - 296
5X-RAY DIFFRACTION5chain 'A' and (resid 297 through 382 )A297 - 382
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 90 )B25 - 90
7X-RAY DIFFRACTION7chain 'B' and (resid 91 through 154 )B91 - 154
8X-RAY DIFFRACTION8chain 'B' and (resid 155 through 204 )B155 - 204
9X-RAY DIFFRACTION9chain 'B' and (resid 205 through 364 )B205 - 364
10X-RAY DIFFRACTION10chain 'B' and (resid 365 through 383 )B365 - 383

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