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- PDB-1cjs: CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L1 FROM METHANOCOCCUS JANN... -

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Basic information

Entry
Database: PDB / ID: 1cjs
TitleCRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L1 FROM METHANOCOCCUS JANNASCHII
Components50S RIBOSOMAL PROTEIN L1PRibosome
KeywordsRIBOSOME / RIBOSOMAL PROTEIN / PRIMARY RRNA-BINDING PROTEIN / TRANSLATIONAL REPRESSOR
Function / homology
Function and homology information


large ribosomal subunit / regulation of translation / tRNA binding / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L1/L10, domain II / Ribosomal protein L1/L10, rRNA-binding domain / Ribosomal protein L1, archaea / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein ...Ribosomal protein L1/L10, domain II / Ribosomal protein L1/L10, rRNA-binding domain / Ribosomal protein L1, archaea / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsNevskaya, N. / Tishchenko, S. / Fedorov, R. / Al-Karadaghi, S. / Liljas, A. / Kraft, A. / Piendl, W. / Garber, M. / Nikonov, S.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Archaeal ribosomal protein L1: the structure provides new insights into RNA binding of the L1 protein family.
Authors: Nevskaya, N. / Tischenko, S. / Fedorov, R. / Al-Karadaghi, S. / Liljas, A. / Kraft, A. / Piendl, W. / Garber, M. / Nikonov, S.
History
DepositionApr 19, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 50S RIBOSOMAL PROTEIN L1P


Theoretical massNumber of molelcules
Total (without water)24,8421
Polymers24,8421
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.407, 39.910, 55.634
Angle α, β, γ (deg.)83.03, 80.25, 74.68
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 50S RIBOSOMAL PROTEIN L1P / Ribosome


Mass: 24842.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: RPLA / Plasmid: PET11A/MJAL1 / Species (production host): Escherichia coli / Gene (production host): MJAL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54050
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 3.02 Å3/Da / Density % sol: 60 %
Crystal growMethod: vapor diffusion / pH: 7.5 / Details: pH 7.50, VAPOR DIFFUSION
Crystal grow
*PLUS
Method: other
Details: Tishchenko, S., (1998) Biochem. Mol. Biol. Int., 45, 349.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0009
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0009 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. obs: 11387 / % possible obs: 89.1 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.052
Reflection shellResolution: 2.3→2.4 Å / % possible all: 77.4
Reflection shell
*PLUS
% possible obs: 78.3 % / Redundancy: 3.74 % / Rmerge(I) obs: 0.105

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Processing

Software
NameVersionClassification
X-PLORmodel building
CCP4model building
Omodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→8 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0.2 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.271 531 5 %
Rwork0.203 --
obs0.203 11079 89.1 %
Displacement parametersBiso mean: 28.87 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1683 0 0 70 1753
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.09
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.95
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.37
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: 2.3→2.4 Å / Total num. of bins used: 8 /
Num. reflection% reflection
Rwork1112 -
obs-77.4 %
Xplor fileSerial no: 1 / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.95
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.37

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