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- PDB-8c0p: Crystal structure of S. aureus BlaR1 sensor domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8c0p
TitleCrystal structure of S. aureus BlaR1 sensor domain in complex with a boronate inhibitor
ComponentsRegulatory protein BlaR1
KeywordsSIGNALING PROTEIN / Antibiotic resistance / Beta-lactam sensor of Staphylococcus aureus / MRSA
Function / homology
Function and homology information


penicillin binding / plasma membrane
Similarity search - Function
: / Peptidase M56 / BlaR1 peptidase M56 / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
: / Regulatory protein BlaR1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMiguel-Ruano, V. / Jimenez-Faraco, E. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-90030-P Spain
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Restoring susceptibility to beta-lactam antibiotics in methicillin-resistant Staphylococcus aureus.
Authors: Nguyen, V.T. / Birhanu, B.T. / Miguel-Ruano, V. / Kim, C. / Batuecas, M. / Yang, J. / El-Araby, A.M. / Jimenez-Faraco, E. / Schroeder, V.A. / Alba, A. / Rana, N. / Sader, S. / Thomas, C.A. / ...Authors: Nguyen, V.T. / Birhanu, B.T. / Miguel-Ruano, V. / Kim, C. / Batuecas, M. / Yang, J. / El-Araby, A.M. / Jimenez-Faraco, E. / Schroeder, V.A. / Alba, A. / Rana, N. / Sader, S. / Thomas, C.A. / Feltzer, R. / Lee, M. / Fisher, J.F. / Hermoso, J.A. / Chang, M. / Mobashery, S.
History
DepositionDec 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
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
Revision 1.2Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein BlaR1
B: Regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4434
Polymers59,5412
Non-polymers9022
Water1,51384
1
A: Regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2222
Polymers29,7701
Non-polymers4511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2222
Polymers29,7701
Non-polymers4511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.904, 106.780, 56.278
Angle α, β, γ (deg.)90.000, 108.092, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Regulatory protein BlaR1


Mass: 29770.432 Da / Num. of mol.: 2 / Mutation: K369A K370A K372A
Source method: isolated from a genetically manipulated source
Details: Triple mutant K369A K370A K372A and acylated-serine 389 with the boronic inhibitor
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: blaR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18357
#2: Chemical ChemComp-SZI / [1-[[2,4-bis(trifluoromethyl)phenyl]methyl]benzimidazol-2-yl]sulfanylmethyl-$l^{3}-oxidanyl-bis(oxidanyl)boron


Mass: 451.171 Da / Num. of mol.: 2 / Mutation: K369A K370A K372A
Source method: isolated from a genetically manipulated source
Formula: C17H14BF6N2O3S
Details: Triple mutant K369A K370A K372A and acylated-serine 389 with the boronic inhibitor
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: blaR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.25
Details: Sodium Cacodylate 0.085M pH 5.25 + PEG 8K 21% + Glycerol 15%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.97→47.83 Å / Num. obs: 36626 / % possible obs: 98.7 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.035 / Net I/σ(I): 10.6
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.578 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2573 / CC1/2: 0.534 / Rpim(I) all: 0.747 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→47.829 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.196 / SU B: 11.918 / SU ML: 0.149 / Average fsc free: 0.9503 / Average fsc work: 0.9631 / Cross valid method: FREE R-VALUE / ESU R: 0.196 / ESU R Free: 0.169
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2367 1814 4.956 %
Rwork0.195 34785 -
all0.197 --
obs-36599 98.398 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.161 Å2
Baniso -1Baniso -2Baniso -3
1--0.031 Å2-0 Å2-0.183 Å2
2--0.021 Å20 Å2
3---0.107 Å2
Refinement stepCycle: LAST / Resolution: 1.97→47.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4214 0 0 84 4298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124380
X-RAY DIFFRACTIONr_bond_other_d0.0040.0163795
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.6635921
X-RAY DIFFRACTIONr_angle_other_deg0.4381.5758899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6795513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.5881010
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01110789
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.01410223
X-RAY DIFFRACTIONr_chiral_restr0.0540.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024897
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02899
X-RAY DIFFRACTIONr_nbd_refined0.2130.2772
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.23424
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22125
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22098
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2122
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.220
X-RAY DIFFRACTIONr_nbd_other0.190.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1550.27
X-RAY DIFFRACTIONr_mcbond_it2.2153.9592040
X-RAY DIFFRACTIONr_mcbond_other2.2133.9592040
X-RAY DIFFRACTIONr_mcangle_it3.4355.9212557
X-RAY DIFFRACTIONr_mcangle_other3.4345.9232558
X-RAY DIFFRACTIONr_scbond_it2.484.3052340
X-RAY DIFFRACTIONr_scbond_other2.4784.3032339
X-RAY DIFFRACTIONr_scangle_it3.9286.3493364
X-RAY DIFFRACTIONr_scangle_other3.9276.353365
X-RAY DIFFRACTIONr_lrange_it5.88652.585021
X-RAY DIFFRACTIONr_lrange_other5.88252.5895016
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.97-2.0210.3531280.34225880.34327440.9020.90698.97960.319
2.021-2.0760.3021180.31424910.31326400.9390.9398.82580.277
2.076-2.1360.3321240.29524420.29725990.9280.9498.73030.256
2.136-2.2020.3431270.26723680.27125280.9210.95398.69460.233
2.202-2.2740.2991240.24522880.24824410.9440.96298.8120.214
2.274-2.3540.2881080.23322490.23623920.9550.96698.53680.201
2.354-2.4420.2841110.21921520.22222790.9510.97199.29790.192
2.442-2.5420.2651030.21220630.21521850.9570.97499.13040.189
2.542-2.6550.299960.21219790.21621010.9530.97498.76250.192
2.655-2.7840.2451000.19719090.19920310.9630.97798.91680.184
2.784-2.9340.242940.18918110.19119250.9660.97998.9610.178
2.934-3.1110.296840.19816900.20218040.9520.97698.3370.195
3.111-3.3250.242860.21116140.21317230.9620.97498.66510.213
3.325-3.590.266860.19814770.20215890.9510.97898.36380.206
3.59-3.930.192740.17413620.17514620.9750.98298.22160.187
3.93-4.390.18720.14412320.14613380.9830.98797.45890.166
4.39-5.0620.172580.13810790.1411800.9840.9996.35590.17
5.062-6.1830.229560.1839030.18610000.9740.98495.90.211
6.183-8.6710.181380.1666930.1667730.9820.98694.56660.196
8.671-47.8290.178270.1643950.1654590.9780.98391.9390.189
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)
11.23110.02450.40690.53980.18430.6930.08580.00260.10550.005-0.016-0.04240.0269-0.0275-0.06980.0203-0.0167-0.00630.03080.02010.042820.04225.21983.873
20.59830.09820.33390.72170.37422.1155-0.0877-0.09190.0001-0.0167-0.1410.00090.2328-0.16780.22870.08530.00930.01530.0389-0.01180.045132.2245-19.364228.0255
Refinement TLS groupSelection: ALL

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