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- PDB-5tw8: Crystal structure of wild-type S. aureus penicillin binding prote... -

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Basic information

Entry
Database: PDB / ID: 5tw8
TitleCrystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4) 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 / 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
Ceftaroline, bound form / Penicillin-binding protein 4
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsAlexander, J.A.N. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health 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 1.2Oct 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_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.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.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)82,0039
Polymers80,5032
Non-polymers1,5007
Water8,665481
1
A: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0555
Polymers40,2511
Non-polymers8044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9484
Polymers40,2511
Non-polymers6963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.415, 92.165, 79.153
Angle α, β, γ (deg.)90.000, 99.230, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-402-

ZN

21B-700-

HOH

DetailsMonomer as determined by size exclusion chromatography

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Components

#1: Protein Penicillin-binding protein 4


Mass: 40251.414 Da / Num. of mol.: 2 / Fragment: residues 25-383
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-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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
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: 1.72→46.08 Å / Num. obs: 87247 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 21.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.066 / Rrim(I) all: 0.128 / Net I/σ(I): 7.8 / Num. measured all: 327221
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.72-1.753.81.4130.612199.7
9.26-46.083.50.0410.996198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.94 Å46.08 Å
Translation5.94 Å46.08 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX`refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TVF

1tvf


Resolution: 1.72→46.08 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.78
RfactorNum. reflection% reflection
Rfree0.2146 4378 5.02 %
Rwork0.1862 --
obs0.1876 87188 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.83 Å2 / Biso mean: 33.3412 Å2 / Biso min: 10.84 Å2
Refinement stepCycle: final / Resolution: 1.72→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5595 0 83 481 6159
Biso mean--79.98 38.45 -
Num. residues----715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065826
X-RAY DIFFRACTIONf_angle_d0.8567908
X-RAY DIFFRACTIONf_chiral_restr0.048888
X-RAY DIFFRACTIONf_plane_restr0.0051025
X-RAY DIFFRACTIONf_dihedral_angle_d12.6153624
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 (%)
1.72-1.73950.34881410.349326962837100
1.7395-1.760.35681640.338327432907100
1.76-1.78150.3691510.318527332884100
1.7815-1.8040.32951540.307627732927100
1.804-1.82780.30881410.301327252866100
1.8278-1.85280.28231460.276127792925100
1.8528-1.87930.31681480.269927292877100
1.8793-1.90730.31841530.27827632916100
1.9073-1.93710.35631590.329627052864100
1.9371-1.96890.25091490.234927602909100
1.9689-2.00280.22131400.227627592899100
2.0028-2.03930.24731560.212627472903100
2.0393-2.07850.26131390.208627792918100
2.0785-2.12090.24821320.19827842916100
2.1209-2.1670.18951360.185627632899100
2.167-2.21740.21261400.188527362876100
2.2174-2.27290.2941350.241727892924100
2.2729-2.33430.23711430.190527522895100
2.3343-2.4030.2171530.175827712924100
2.403-2.48060.17561550.164527872942100
2.4806-2.56920.21611360.167427362872100
2.5692-2.67210.24061300.170527732903100
2.6721-2.79370.21841490.17627482897100
2.7937-2.9410.20741300.17127962926100
2.941-3.12520.20191550.16872749290499
3.1252-3.36640.21021380.167127762914100
3.3664-3.70510.19851470.148527862933100
3.7051-4.24090.141540.132827642918100
4.2409-5.34180.14311510.134827982949100
5.3418-46.0990.19441530.17412811296499
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)
10.9272-0.7216-0.54962.58450.76531.8072-0.01170.0992-0.0725-0.00860.0010.21250.0011-0.1794-0.00350.0596-0.0174-0.02220.14610.00230.111929.0386-47.022340.9974
22.14722.54041.66058.2074-0.12772.86470.0067-0.1133-0.0647-0.10460.04160.0505-0.04680.0046-0.07290.16650.0029-0.01730.2002-0.050.138831.3933-68.717523.4786
31.0527-0.3906-0.00823.69260.56741.3160.00920.1142-0.1358-0.0240.02480.23810.0808-0.1855-0.03050.1575-0.0423-0.00290.1958-0.01620.141630.944-55.95734.1818
44.1291.3351-0.92753.4897-1.23912.7580.09530.46070.5894-0.0324-0.0262-0.1134-0.36980.1674-0.04350.25280.00280.00070.17750.03440.186938.9966-29.277633.7657
52.8173-3.17-0.68664.354-0.57076.1376-0.1576-0.5504-0.20140.70350.36140.69650.1227-0.2897-0.08730.36380.0640.08490.179-0.01310.22928.1022-39.03176.8865
60.6203-0.0943-0.18972.0280.53311.063-0.1388-0.0808-0.04340.17070.109-0.04390.296-0.05490.01170.26380.0426-0.01040.17170.01080.12941.2661-55.8146-8.8979
72.79180.02832.43184.8716-0.51223.0031-0.091-0.1493-0.16760.09820.2120.29590.4842-0.3088-0.07870.3613-0.03340.04460.20260.00830.149236.3172-65.069-14.3513
82.39411.48710.88067.82910.67123.6446-0.0488-0.186-0.13420.73020.0399-0.20520.4279-0.06610.04330.34540.1002-0.03190.1920.00360.144945.5753-62.2987-0.36
94.31651.12361.38683.34851.25283.4196-0.12170.2460.0377-0.04910.1330.10040.2073-0.0443-0.02120.23240.05280.00070.11260.01150.111636.7474-50.2732-13.0183
106.2531-3.4474.02785.7952-4.68238.5703-0.08-0.0395-0.06230.01130.24130.34590.4712-0.5509-0.18880.2693-0.02020.03340.1505-0.02090.149727.3535-48.2471-7.03
113.74290.08571.12325.8021-1.1255.4085-0.0216-0.2605-0.16460.50880.14390.50520.401-0.2592-0.07680.19870.05340.05190.1169-0.01730.141731.3753-45.593-1.4007
127.75036.4059-3.54477.7165-3.45193.1437-0.06870.25160.2989-0.0020.08270.026-0.02710.0746-0.05660.17130.0617-0.04150.17640.03050.172540.289-27.843-6.5713
136.3042.9871-1.66625.77270.31718.06460.0610.06920.4857-0.1665-0.04520.2799-0.38510.2886-0.10420.18320.0028-0.06540.12110.00430.256549.0321-22.2259-5.5832
143.82031.4452-1.42017.001-1.59887.41620.03740.2535-0.1057-0.0483-0.1058-0.60160.16770.44470.06830.08380.0464-0.07360.2262-0.04510.277352.2689-29.881-3.9489
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 154 )A91 - 154
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 296 )A155 - 296
4X-RAY DIFFRACTION4chain 'A' and (resid 297 through 382 )A297 - 382
5X-RAY DIFFRACTION5chain 'B' and (resid 25 through 56 )B25 - 56
6X-RAY DIFFRACTION6chain 'B' and (resid 57 through 111 )B57 - 111
7X-RAY DIFFRACTION7chain 'B' and (resid 112 through 154 )B112 - 154
8X-RAY DIFFRACTION8chain 'B' and (resid 155 through 204 )B155 - 204
9X-RAY DIFFRACTION9chain 'B' and (resid 205 through 239 )B205 - 239
10X-RAY DIFFRACTION10chain 'B' and (resid 240 through 266 )B240 - 266
11X-RAY DIFFRACTION11chain 'B' and (resid 267 through 296 )B267 - 296
12X-RAY DIFFRACTION12chain 'B' and (resid 297 through 335 )B297 - 335
13X-RAY DIFFRACTION13chain 'B' and (resid 336 through 364 )B336 - 364
14X-RAY DIFFRACTION14chain 'B' and (resid 365 through 383 )B365 - 383

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