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- PDB-8cf3: Crystal structure of S. aureus BlaR1 sensor domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8cf3
TitleCrystal structure of S. aureus BlaR1 sensor domain in complex with cefepime
ComponentsRegulatory protein BlaR1
KeywordsSIGNALING PROTEIN / Antibiotic resistance / Beta-lactam sensor of Staphylococcus aureus / MRSA
Function / homology
Function and homology information


penicillin binding / cell wall organization / 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: 2.52 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
DepositionFeb 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Regulatory protein BlaR1
E: Regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8854
Polymers58,9142
Non-polymers9712
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-3 kcal/mol
Surface area23210 Å2
Unit cell
Length a, b, c (Å)46.819, 109.470, 50.297
Angle α, β, γ (deg.)90.000, 103.657, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 333 - 583 / Label seq-ID: 1 - 251

Dom-IDAuth asym-IDLabel asym-ID
1CA
2EB

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

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Components

#1: Protein Regulatory protein BlaR1


Mass: 29457.121 Da / Num. of mol.: 2 / Mutation: Triple mutant K369A K370A K372A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: blaR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18357
#2: Chemical ChemComp-UJ9 / Cefepime (open) / (2R,5S)-2-[(1R)-1-[[(2Z)-2-(2-azanyl-1,3-thiazol-4-yl)-2-methoxyimino-ethanoyl]amino]-2-oxidanyl-ethyl]-5-[(1-methylpyrrolidin-1-ium-1-yl)methyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / Cefepimum (reacted)


Mass: 485.601 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H29N6O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.11 Å3/Da / Density % sol: 41.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.25
Details: Soidum Cacodylate 0.085M pH 5.5 + PEG 8K 27% + Glycerol 15%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0064 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0064 Å / Relative weight: 1
ReflectionResolution: 2.153→45.537 Å / Num. obs: 17584 / % possible obs: 82.55 % / Redundancy: 6.05 % / CC1/2: 0.9969 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.057 / Rrim(I) all: 0.142 / Net I/σ(I): 9.186
Reflection shellResolution: 2.153→2.345 Å / Rmerge(I) obs: 1.772 / Num. unique obs: 880 / CC1/2: 0.3028 / Rpim(I) all: 0.865

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→45.537 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.888 / SU B: 35.026 / SU ML: 0.356 / Cross valid method: FREE R-VALUE / ESU R Free: 0.391
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.27 778 5.148 %
Rwork0.2165 14334 -
all0.219 --
obs-15112 90.605 %
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: 54.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.294 Å20 Å23.124 Å2
2--3.39 Å20 Å2
3----4.127 Å2
Refinement stepCycle: LAST / Resolution: 2.52→45.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 76 59 4275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124326
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163950
X-RAY DIFFRACTIONr_angle_refined_deg0.9171.6725832
X-RAY DIFFRACTIONr_angle_other_deg0.3381.6049112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1135500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.438510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56710778
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.8510220
X-RAY DIFFRACTIONr_chiral_restr0.0790.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021050
X-RAY DIFFRACTIONr_nbd_refined0.1920.2866
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.23670
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22089
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2134
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1290.210
X-RAY DIFFRACTIONr_nbd_other0.2370.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2020.22
X-RAY DIFFRACTIONr_mcbond_it1.1132.5172006
X-RAY DIFFRACTIONr_mcbond_other1.1132.5172006
X-RAY DIFFRACTIONr_mcangle_it2.0124.5182504
X-RAY DIFFRACTIONr_mcangle_other2.0124.5192505
X-RAY DIFFRACTIONr_scbond_it0.912.6022320
X-RAY DIFFRACTIONr_scbond_other0.912.6032321
X-RAY DIFFRACTIONr_scangle_it1.6794.7443328
X-RAY DIFFRACTIONr_scangle_other1.6794.7463329
X-RAY DIFFRACTIONr_lrange_it3.50724.5364997
X-RAY DIFFRACTIONr_lrange_other3.48324.5194986
X-RAY DIFFRACTIONr_ncsr_local_group_10.080.059079
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11CX-RAY DIFFRACTIONLocal ncs0.079540.05011
12EX-RAY DIFFRACTIONLocal ncs0.079540.05011
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
2.52-2.5850.339470.2796880.28212250.9470.958600.241
2.585-2.6560.275420.2657820.26611900.9390.96469.24370.218
2.656-2.7330.292390.2998700.29811680.9450.94977.82530.258
2.733-2.8160.385560.2768730.28311070.9160.9683.92050.226
2.816-2.9080.297580.2739520.27411160.9490.96390.50180.214
2.908-3.010.399570.2679320.27410420.9080.96594.91360.213
3.01-3.1230.334460.2559890.25810440.9350.96699.13790.207
3.123-3.250.28550.2548940.2569610.9530.96498.75130.209
3.25-3.3940.33520.2228900.2289560.9340.97398.53560.188
3.394-3.5580.218400.228590.229100.9770.97798.79120.184
3.558-3.750.236380.2087990.2098470.9580.97898.81940.183
3.75-3.9750.198420.1927700.1938170.9850.9899.3880.175
3.975-4.2470.175360.1657370.1667820.9780.98598.84910.158
4.247-4.5840.273320.1736750.1777140.9610.98399.01960.169
4.584-5.0170.254340.1746090.1796530.9640.98398.46860.172
5.017-5.6010.277230.2035680.2065950.9710.97899.32770.197
5.601-6.4510.312190.2495050.2525270.9420.9799.43070.243
6.451-7.8610.285260.2544230.2564530.9570.96599.1170.25
7.861-10.9550.267190.1453310.1523540.960.98698.87010.151
10.955-45.5370.239170.2181840.222120.9780.97494.81130.228
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)
12.57140.14870.98921.3421-0.27951.72530.0476-0.03610.164-0.0522-0.0555-0.05010.0076-0.1020.00790.304-0.0146-0.24160.0167-0.01360.467820.97937.2374.3098
21.4801-0.53020.73691.1046-0.29882.6087-0.0596-0.2303-0.1028-0.14470.0403-0.04180.1156-0.09340.01930.34370.0232-0.26220.0380.01540.437535.686-18.367525.3951
Refinement TLS groupSelection: ALL

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