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- PDB-3q82: Meropenem acylated BlaR1 sensor domain from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 3q82
TitleMeropenem acylated BlaR1 sensor domain from Staphylococcus aureus
ComponentsBeta-lactamase regulatory protein BlaR1
KeywordsHYDROLASE REGULATOR/ANTIBIOTIC / antibiotic-binding / MRSA / antibiotic-binding-antibiotic complex / HYDROLASE REGULATOR-ANTIBIOTIC complex
Function / homology
Function and homology information


penicillin binding / integral component of membrane / plasma membrane
Similarity search - Function
BlaR1 peptidase M56 / Peptidase M56 / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MER / Regulatory protein BlaR1 / Beta-lactam sensor/signal transducer BlaR1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsBorbulevych, O.Y. / Mobashery, S. / Baker, B.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Lysine Nzeta-decarboxylation switch and activation of the beta-lactam sensor domain of BlaR1 protein of methicillin-resistant Staphylococcus aureus.
Authors: Borbulevych, O. / Kumarasiri, M. / Wilson, B. / Llarrull, L.I. / Lee, M. / Hesek, D. / Shi, Q. / Peng, J. / Baker, B.M. / Mobashery, S.
History
DepositionJan 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Non-polymer description
Revision 1.2Jan 9, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase regulatory protein BlaR1
B: Beta-lactamase regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4029
Polymers59,1712
Non-polymers1,2317
Water2,288127
1
A: Beta-lactamase regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1554
Polymers29,5851
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2475
Polymers29,5851
Non-polymers6624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.801, 108.087, 56.451
Angle α, β, γ (deg.)90.00, 108.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase regulatory protein BlaR1 / Bla regulator protein blaR1


Mass: 29585.252 Da / Num. of mol.: 2 / Fragment: residues 332-583
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: blaR1, VRA0048 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7WU28, UniProt: P18357*PLUS
#2: Chemical ChemComp-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form / Meropenem


Mass: 385.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O5S / Comment: antibiotic*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG4000 30%, TRIS 0.1M, NH4SSO4 0.2M, pH 8.5, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 12, 2010
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 30922 / Num. obs: 28047 / % possible obs: 90.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.142.90.301162
2.14-2.1730.251165.3
2.17-2.223.10.261170.1
2.22-2.263.10.239175.7
2.26-2.313.20.224179.5
2.31-2.363.30.217184.7
2.36-2.423.50.196188.1
2.42-2.493.50.18193.3
2.49-2.563.50.174198.3
2.56-2.643.70.149199.9
2.64-2.743.80.1291100
2.74-2.853.80.1131100
2.85-2.983.80.1021100
2.98-3.133.80.088199.9
3.13-3.333.80.0811100
3.33-3.593.80.0751100
3.59-3.943.70.074199.5
3.94-4.513.60.052197.8
4.51-5.663.70.038198.9
5.66-203.70.0511100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.368 / SU ML: 0.137 / SU R Cruickshank DPI: 0.2813 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23405 1406 5 %RANDOM
Rwork0.18336 ---
obs0.18586 26615 90.34 %-
all-31017 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.195 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-2.34 Å2
2---0.88 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4172 0 82 127 4381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224357
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9525867
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5275502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55425.225222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78815782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5451510
X-RAY DIFFRACTIONr_chiral_restr0.1230.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023316
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6781.52502
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27224022
X-RAY DIFFRACTIONr_scbond_it2.24231855
X-RAY DIFFRACTIONr_scangle_it3.6094.51845
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.098→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 71 -
Rwork0.21 1292 -
obs--60.1 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.8303-0.51510.67941.89940.1251.9966-0.0192-0.07880.0320.1069-0.00160.03340.0063-0.01660.02070.0077-0.00380.00260.0092-0.00240.0015-6.275-0.66223.169
21.5010.22490.03522.4297-0.61153.0413-0.01850.0897-0.0952-0.0732-0.04020.00550.11190.0540.05870.05920.004-0.03660.02560.00840.0596-17.591-25.297-1.028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 254
2X-RAY DIFFRACTION2B2 - 254

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