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- PDB-8c0s: Crystal structure of S. aureus BlaR1 sensor domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8c0s
TitleCrystal structure of S. aureus BlaR1 sensor domain in complex with an imidazole inhibitor
ComponentsRegulatory protein BlaR1
KeywordsSIGNALING PROTEIN / Antibiotic resistance / b-lactam sensor / 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: 2 Å
AuthorsMiguel-Ruano, V. / 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

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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)60,2534
Polymers59,5412
Non-polymers7132
Water1,24369
1
A: Regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1272
Polymers29,7701
Non-polymers3561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1272
Polymers29,7701
Non-polymers3561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.027, 107.943, 56.390
Angle α, β, γ (deg.)90.000, 109.454, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 333 - 582 / Label seq-ID: 2 - 251

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Regulatory protein BlaR1


Mass: 29770.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Triple mutant K369A K370A K372A / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: blaR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18357
#2: Chemical ChemComp-SYU / 3-[[2,4-bis(trifluoromethyl)phenyl]methyl]-5-(hydroxymethyl)-1~{H}-imidazole-2-thione


Mass: 356.287 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10F6N2OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Sodium Cacodylate 0.085M pH 6.0 + 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: Oct 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→47.7 Å / Num. obs: 35815 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.022 / Net I/σ(I): 15.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.758 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2645 / CC1/2: 0.589 / Rpim(I) all: 0.767 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.698 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.185 / SU B: 12.7 / SU ML: 0.154 / Average fsc free: 0.9467 / Average fsc work: 0.9614 / Cross valid method: FREE R-VALUE / ESU R: 0.193 / ESU R Free: 0.168
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2323 1797 5.022 %
Rwork0.1876 33988 -
all0.19 --
obs-35785 99.891 %
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: 58.404 Å2
Baniso -1Baniso -2Baniso -3
1--0.009 Å20 Å20.008 Å2
2---0.011 Å20 Å2
3---0.012 Å2
Refinement stepCycle: LAST / Resolution: 2→47.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4156 0 33 69 4258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124333
X-RAY DIFFRACTIONr_bond_other_d0.0070.0163782
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.6455843
X-RAY DIFFRACTIONr_angle_other_deg0.4671.578871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5735509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.6111010
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03410790
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.34510222
X-RAY DIFFRACTIONr_chiral_restr0.0610.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02890
X-RAY DIFFRACTIONr_nbd_refined0.2070.2835
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.23474
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22076
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22160
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.295
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.218
X-RAY DIFFRACTIONr_nbd_other0.1930.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.090.27
X-RAY DIFFRACTIONr_mcbond_it4.2924.9562030
X-RAY DIFFRACTIONr_mcbond_other4.2834.9562030
X-RAY DIFFRACTIONr_mcangle_it5.9017.4012541
X-RAY DIFFRACTIONr_mcangle_other5.97.4032542
X-RAY DIFFRACTIONr_scbond_it4.7465.5152303
X-RAY DIFFRACTIONr_scbond_other4.7455.5152304
X-RAY DIFFRACTIONr_scangle_it6.9858.073302
X-RAY DIFFRACTIONr_scangle_other7.1428.0683303
X-RAY DIFFRACTIONr_lrange_it9.39466.774965
X-RAY DIFFRACTIONr_lrange_other9.39366.7754960
X-RAY DIFFRACTIONr_ncsr_local_group_10.0740.058801
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.074370.0501
12AX-RAY DIFFRACTIONLocal ncs0.074370.0501
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
2-2.0520.3721250.36425120.36426380.8730.88999.96210.328
2.052-2.1080.3641140.34624430.34725600.8790.91199.88280.301
2.108-2.1690.3591200.30324050.30525300.9150.93599.80240.258
2.169-2.2360.2861240.26222910.26324180.9460.95299.87590.214
2.236-2.3090.3231170.24922230.25223430.9330.9699.8720.203
2.309-2.390.2431260.22921430.2322690.9620.9681000.191
2.39-2.480.2681030.20621230.20922260.9530.9751000.169
2.48-2.5810.2511170.20219780.20520960.9610.97799.95230.166
2.581-2.6950.2291260.18619080.18920340.9680.9811000.161
2.695-2.8260.27940.1918380.19419320.9580.9791000.173
2.826-2.9780.22790.1817840.18218640.9650.98199.94640.166
2.978-3.1580.2641070.20516520.20917600.9620.97499.94320.196
3.158-3.3750.247620.19715750.19916380.960.97899.93890.194
3.375-3.6440.25680.18514550.18715250.9650.98199.86890.187
3.644-3.990.212750.16713530.16914280.9770.9851000.175
3.99-4.4570.207630.14712070.1512740.9780.98799.6860.162
4.457-5.1380.162630.13910710.1411350.9850.9999.91190.16
5.138-6.2750.294490.1979090.2029610.9590.98199.68780.223
6.275-8.7990.186360.1847050.1847480.9740.98399.06420.215
8.799-47.6980.172290.1424130.1444430.9780.98699.77430.166
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)
11.16940.13850.39810.6866-0.05480.7250.05270.00540.0402-0.01670.0052-0.00770.0053-0.0423-0.05790.013-0.0196-0.00770.05810.01560.059220.20576.51363.7836
20.6413-0.09140.17110.9753-0.1061.1971-0.0856-0.1299-0.0416-0.0505-0.0021-0.06950.0462-0.11170.08770.10540.0316-0.0360.0356-0.00670.046931.6473-18.545427.6655
Refinement TLS groupSelection: ALL

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