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- PDB-1bxe: RIBOSOMAL PROTEIN L22 FROM THERMUS THERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1bxe
TitleRIBOSOMAL PROTEIN L22 FROM THERMUS THERMOPHILUS
ComponentsPROTEIN (RIBOSOMAL PROTEIN L22)
KeywordsRNA BINDING PROTEIN / RIBOSOMAL PROTEIN / PROTEIN SYNTHESIS / RNA BINDING / ANTIBIOTICS RESISTANCE
Function / homology
Function and homology information


large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L22/L17 / Ribosomal Protein L22; Chain A / Ribosomal protein L22, bacterial/chloroplast-type / : / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L22p/L17e / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein uL22
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsUnge, J. / Aberg, A. / Al-Karadaghi, S. / Nikulin, A. / Nikonov, S. / Davydova, N. / Nevskaya, N. / Garber, M. / Liljas, A.
CitationJournal: Structure / Year: 1998
Title: The crystal structure of ribosomal protein L22 from Thermus thermophilus: insights into the mechanism of erythromycin resistance.
Authors: Unge, J. / berg, A. / Al-Kharadaghi, S. / Nikulin, A. / Nikonov, S. / Davydova, N. / Nevskaya, N. / Garber, M. / Liljas, A.
History
DepositionOct 2, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 7, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (RIBOSOMAL PROTEIN L22)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0084
Polymers12,9021
Non-polymers1063
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.640, 65.930, 67.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (RIBOSOMAL PROTEIN L22)


Mass: 12901.846 Da / Num. of mol.: 1 / Mutation: MET1MSE, MET64MSE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Cellular location: RIBOSOME / Production host: Escherichia coli (E. coli) / References: UniProt: P48286
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growpH: 7 / Details: pH 7
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
22.0 Mammonium hydrogen phosphate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.012
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.012 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 12173 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.053
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.159 / % possible all: 94.8
Reflection shell
*PLUS
% possible obs: 94.8 %

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 -10 %RANDOM
Rwork0.189 ---
obs0.189 15976 98 %-
Displacement parametersBiso mean: 20.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 3 63 948
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.34
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.32
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.71
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.31 69 -
Rwork0.26 1336 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAMETER.ELEMENTS
X-RAY DIFFRACTION3PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.32
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.71

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