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- PDB-1dwu: Ribosomal protein L1 -

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Basic information

Entry
Database: PDB / ID: 1dwu
TitleRibosomal protein L1
ComponentsRIBOSOMAL PROTEIN L1
KeywordsRIBOSOMAL PROTEIN / RNA BINDING / PROTEIN SYNTHESIS
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
50S ribosomal protein L1
Similarity search - Component
Biological speciesMETHANOCOCCUS THERMOLITHOTROPHICUS (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTishchenko, S.V. / Nevskaya, N.A. / Pavelyev, M.N. / Nikonov, S.V. / Garber, M.B. / Piendl, W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of Ribosomal Protein L1 from Methanococcus Thermolithotrophicus. Functionally Important Structural Invariants on the L1 Surface
Authors: Nevskaya, N.A. / Tishchenko, S.V. / Paveliev, M. / Smolinskaya, Y. / Fedorov, R. / Piendl, W. / Nakamura, Y. / Toyoda, T. / Garber, M.B. / Nikonov, S.V.
History
DepositionDec 13, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOMAL PROTEIN L1
B: RIBOSOMAL PROTEIN L1


Theoretical massNumber of molelcules
Total (without water)47,6642
Polymers47,6642
Non-polymers00
Water0
1
A: RIBOSOMAL PROTEIN L1


Theoretical massNumber of molelcules
Total (without water)23,8321
Polymers23,8321
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RIBOSOMAL PROTEIN L1


Theoretical massNumber of molelcules
Total (without water)23,8321
Polymers23,8321
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.360, 69.980, 106.170
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 RIBOSOMAL PROTEIN L1 /


Mass: 23831.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCOCCUS THERMOLITHOTROPHICUS (archaea)
Strain: SN-1 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Cellular location: RIBOSOME / Gene: THE CORRESPONDING GENE IN E. COLI IS RPLA / Plasmid: PMTHL1.4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O52704

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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: 2.63 Å3/Da / Density % sol: 53 %
Crystal growpH: 5.5
Details: 10% PEG 4K, 40MM MGCL2, 50MM NAAC PH 5.5, 50MM NACL, AGAINST: 30% PEG 4K, 100 MM NAAC
Crystal grow
*PLUS
Temperature: 277 K / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125-30 mg/mlprotein1drop
230 %PEG40001dropprecipitant
30.1 MTris-HCl1dropprecipitant
40.2 M1dropprecipitantCH3COONa
530 %PEG40001reservoir
60.1 M1reservoirCH3COONa

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: R-AXIS IV / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.68→31.01 Å / Num. obs: 13590 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 4.31 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.68→2.77 Å / % possible all: 78.3
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / Num. obs: 14280 / % possible obs: 94.6 % / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 81.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.275

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CJS

1cjs


Resolution: 2.8→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: X-PLOR V3.1F WAS ALSO USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.305 557 5 %RANDOM
Rwork0.207 ---
obs0.207 11147 91 %-
Displacement parametersBiso mean: 37.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 0 0 0 3336
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.703
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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: 2.8→2.92 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.41 56 -
Rwork0.33 1144 -
obs--81 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / Num. reflection obs: 12624 / % reflection Rfree: 8.9 % / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 53 Å2

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