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- PDB-1i2a: CRYSTAL STRUCTURE OF L1 RIBOSOMAL PROTEIN FROM METHANOCOCCUS JANN... -

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Basic information

Entry
Database: PDB / ID: 1i2a
TitleCRYSTAL STRUCTURE OF L1 RIBOSOMAL PROTEIN FROM METHANOCOCCUS JANNASCHII WITH 1.85A RESOLUTION.
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
PENTANAL / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSmolinskaya, Y. / Nikonov, S.V.
Citation
#1: Journal: Structure / 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.
#2: Journal: 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. / Tishchenko, S. / Paveliev, M. / Smolinskaya, Y. / Fedorov, R. / Piendl, W. / Nakamura, Y. / Toyoda, T. / Garber, M. / Nikonov, S.
History
DepositionFeb 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 31, 2011Group: Atomic model
Revision 1.4Mar 12, 2014Group: Database references
Revision 1.5Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S RIBOSOMAL PROTEIN L1P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9292
Polymers24,8421
Non-polymers861
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.577, 38.881, 54.936
Angle α, β, γ (deg.)83.32, 80.14, 74.72
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54050
#2: Chemical ChemComp-PTL / PENTANAL / Pentanal


Mass: 86.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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 growTemperature: 301.5 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 10000, HEPES-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 301.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.009 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 17, 1999
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.825→20 Å / Num. all: 188639 / Num. obs: 23155 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.52 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 15
Reflection shellResolution: 1.825→2 Å / Redundancy: 3.41 % / Rmerge(I) obs: 0.309 / % possible all: 87.1

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CJS

1cjs


Resolution: 1.85→19.83 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 673607.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1078 4.8 %RANDOM
Rwork0.222 ---
all0.222 23405 --
obs0.222 22327 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.13 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.18 Å21.85 Å2-0.83 Å2
2--2.27 Å20.48 Å2
3----3.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1682 0 6 185 1873
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it3.211.5
X-RAY DIFFRACTIONc_mcangle_it4.862
X-RAY DIFFRACTIONc_scbond_it5.762
X-RAY DIFFRACTIONc_scangle_it8.512.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 166 4.5 %
Rwork0.298 3541 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMALD.TOP
X-RAY DIFFRACTION3ALD_OLD.PARAM

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