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- PDB-5tw4: Crystal structure of S. aureus penicillin binding protein 4 (PBP4... -

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Basic information

Entry
Database: PDB / ID: 5tw4
TitleCrystal structure of S. aureus penicillin binding protein 4 (PBP4) mutant (E183A, F241R) in complex with ceftaroline
ComponentsPenicillin-binding protein 4
KeywordsHYDROLASE / Antibiotic / Hydrolase / Penicillin binding protein / beta-lactam antibiotics / HYDROLASE - Antibiotic complex
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase activity / beta-lactam antibiotic catabolic process / beta-lactamase activity / 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 / 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
Ceftaroline, bound form / Penicillin-binding protein 4
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 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 11, 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
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_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.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_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)82,11614
Polymers80,4072
Non-polymers1,70912
Water14,772820
1
A: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0276
Polymers40,2031
Non-polymers8245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0898
Polymers40,2031
Non-polymers8857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.696, 92.562, 79.592
Angle α, β, γ (deg.)90.000, 99.750, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-917-

HOH

DetailsMonomer as determined by size exclusion chromatography

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 832 molecules

#2: Chemical ChemComp-AI8 / Ceftaroline, bound form


Mass: 607.729 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23N8O5S4
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 820 / 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: 2.61 Å3/Da / Density % sol: 52.91 %
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: 1.57→46.28 Å / Num. obs: 114289 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.044 / Rrim(I) all: 0.086 / Net I/σ(I): 12.6 / Num. measured all: 436665 / Scaling rejects: 1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.57-1.63.81.0110.625198.4
8.6-46.283.60.0260.998198.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.86 Å46.28 Å
Translation5.86 Å46.28 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
Aimless0.5.17data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TVF

1tvf


Resolution: 1.57→46.28 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.52
RfactorNum. reflection% reflection
Rfree0.1773 5799 5.08 %
Rwork0.1561 --
obs0.1572 114248 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.66 Å2 / Biso mean: 22.6786 Å2 / Biso min: 8.01 Å2
Refinement stepCycle: final / Resolution: 1.57→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5598 0 93 820 6511
Biso mean--29.47 33.43 -
Num. residues----718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085924
X-RAY DIFFRACTIONf_angle_d0.9948062
X-RAY DIFFRACTIONf_chiral_restr0.058907
X-RAY DIFFRACTIONf_plane_restr0.0061053
X-RAY DIFFRACTIONf_dihedral_angle_d11.873687
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 (%)
1.57-1.58780.32821960.3083555375198
1.5878-1.60650.30651980.28923573377198
1.6065-1.62610.29322010.2763537373898
1.6261-1.64670.27891990.26133583378299
1.6467-1.66840.27552000.26223530373099
1.6684-1.69120.25821770.24143643382099
1.6912-1.71540.2332090.22683550375999
1.7154-1.7410.22871770.20943590376799
1.741-1.76820.23382260.20123604383099
1.7682-1.79720.22791840.19743558374299
1.7972-1.82820.19342010.18763559376099
1.8282-1.86140.18031870.17573645383299
1.8614-1.89720.2031920.17343632382499
1.8972-1.9360.22292180.16773542376099
1.936-1.97810.19161950.1593608380399
1.9781-2.02410.18221880.15883610379899
2.0241-2.07470.1711870.14593624381199
2.0747-2.13080.16751790.139436173796100
2.1308-2.19350.15531900.134636663856100
2.1935-2.26430.16781640.131336623826100
2.2643-2.34520.15091900.132736103800100
2.3452-2.43910.1522030.128336383841100
2.4391-2.55010.15191910.130836443835100
2.5501-2.68450.1821820.139436693851100
2.6845-2.85270.18651880.144136533841100
2.8527-3.07290.15571970.137536573854100
3.0729-3.38210.16191800.143336603840100
3.3821-3.87130.15611950.134536603855100
3.8713-4.87650.12012050.120436613866100
4.8765-46.30110.17322000.16393709390999
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)
10.59680.234-0.31841.8054-0.5141.142-0.0263-0.03180.0001-0.05490.0147-0.1149-0.03220.10090.00080.0513-0.0003-0.01750.1095-0.010.078722.7738-47.5586-2.1763
21.8331-2.0678-0.71034.26810.47510.92070.10.2088-0.18150.1554-0.08460.2653-0.0135-0.1864-0.00890.11660.03550.00580.1740.01620.118616.9858-71.607318.1493
30.2278-0.21490.59622.58-0.38161.5053-0.02720.0305-0.02830.02370.0503-0.1994-0.05780.0961-0.01790.13660.01020.0040.16570.01620.139822.382-69.015913.9128
41.0338-0.2292-0.09474.5516-0.51071.47020.0161-0.0057-0.1094-0.19940.00630.17370.13760.04-0.02520.07530.0007-0.03280.11350.00490.111312.807-66.1493-0.0426
51.03480.16150.18551.874-0.4831.3940.0069-0.1356-0.07880.1465-0.0107-0.23290.04310.20410.01660.10950.0155-0.0260.1457-0.00090.126225.8369-52.3737.5959
62.2137-0.7482-0.23362.43040.40851.4210.037-0.240.48190.1026-0.00170.0893-0.2039-0.1328-0.05280.133-0.00530.00710.1366-0.04080.182512.8521-30.16055.5647
71.86941.6727-0.96243.076-0.04843.8684-0.05680.2448-0.0991-0.54380.1494-0.41970.02490.1804-0.08790.2691-0.01890.05490.1123-0.00120.151236.5695-39.2686-46.1192
80.2820.0047-0.16241.629-0.3710.9387-0.07290.0277-0.0478-0.12940.025-0.02170.26680.03420.04640.175-0.0169-0.00040.1167-0.01440.098226.2612-59.4634-28.2584
90.60220.2708-0.10061.78580.01790.76-0.04720.0138-0.0809-0.21910.0337-0.03210.18390.01630.01390.1782-0.0104-0.00090.1111-0.00410.081327.4438-55.2376-33.6486
103.6326-1.7944-0.78792.74170.47991.2180.0565-0.16070.3686-0.06820.05160.0696-0.1012-0.1001-0.10210.1388-0.0278-0.00370.1206-0.00180.131419.1959-27.3431-33.3338
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 383 )A297 - 383
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 56 )B25 - 56
8X-RAY DIFFRACTION8chain 'B' and (resid 57 through 137 )B57 - 137
9X-RAY DIFFRACTION9chain 'B' and (resid 138 through 296 )B138 - 296
10X-RAY DIFFRACTION10chain 'B' and (resid 297 through 383 )B297 - 383

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