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- PDB-1nrf: C-terminal domain of the Bacillus licheniformis BlaR penicillin-r... -

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Basic information

Entry
Database: PDB / ID: 1nrf
TitleC-terminal domain of the Bacillus licheniformis BlaR penicillin-receptor
ComponentsREGULATORY PROTEIN BLAR1
KeywordsMEMBRANE PROTEIN / Penicillin-receptor / Beta-lactamase induction / Bacillus licheniformis / Penicillin-Binding Protein
Function / homology
Function and homology information


penicillin binding / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Peptidase M56 / BlaR1 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
Regulatory protein BlaR1
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKerff, F. / Charlier, P. / Columbo, M.L. / Sauvage, E. / Brans, A. / Frere, J.M. / Joris, B. / Fonze, E.
Citation
Journal: Biochemistry / Year: 2003
Title: Crystal structure of the sensor domain of the BlaR penicillin receptor from Bacillus licheniformis.
Authors: Kerff, F. / Charlier, P. / Colombo, M.L. / Sauvage, E. / Brans, A. / Frere, J.M. / Joris, B. / Fonze, E.
#1: Journal: MOL.MICROBIOL. / Year: 1997
Title: The penicillin sensory transducer, BlaR, involved in the inducibility of beta-lactamase synthesis in Bacillus licheniformis is embedded in the plasma membrane via a four-alpha-helix bundle
Authors: Hardt, K. / Joris, B. / Lepage, S. / Brasseur, R. / Lampen, J.O. / Frere, J.M. / Fink, A.L. / Ghuysen, J.M.
History
DepositionJan 24, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REGULATORY PROTEIN BLAR1


Theoretical massNumber of molelcules
Total (without water)29,9021
Polymers29,9021
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.848, 45.848, 130.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein REGULATORY PROTEIN BLAR1


Mass: 29902.072 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: 749-I / Gene: blaR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P12287
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.34 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.95
Details: 18% PEG 8000, 5% Glycerol, 50mM CaCl2 in 0.1M Cacodylate, pH 6.95, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein1drop
218 %PEG80001reservoir
35 %glycerol1reservoir
450 mM1reservoirCaCl2
50.1 Mcacodylate1reservoirpH6.95

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9786 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.44→32.444 Å / Num. all: 9979 / Num. obs: 9979 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.059 / Net I/σ(I): 8.9
Reflection shellResolution: 2.44→2.5 Å / Redundancy: 4 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 3.7 / Num. unique all: 745 / Rsym value: 0.201 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 32.44 Å / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 99.9 % / Num. unique obs: 745

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Class D beta-lactamase OXA-2 from Salmonella typhimurium

Resolution: 2.5→31.52 Å / Rfactor Rfree error: 0.012 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 442 5 %RANDOM
Rwork0.204 ---
all-9234 --
obs-8827 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.7379 Å2 / ksol: 0.367659 e/Å3
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20 Å20 Å2
2--1.85 Å20 Å2
3----3.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.5→31.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 0 81 2085
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.721.5
X-RAY DIFFRACTIONc_mcangle_it2.792
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 77 5.7 %
Rwork0.213 1284 -
obs-1284 89.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 31.5 Å / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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