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- PDB-1rl2: RIBOSOMAL PROTEIN L2 RNA-BINDING DOMAIN FROM BACILLUS STEAROTHERM... -

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Basic information

Entry
Database: PDB / ID: 1rl2
TitleRIBOSOMAL PROTEIN L2 RNA-BINDING DOMAIN FROM BACILLUS STEAROTHERMOPHILUS
ComponentsPROTEIN (RIBOSOMAL PROTEIN L2)
KeywordsRIBOSOMAL PROTEIN / RNA-BINDING DOMAIN / PEPTIDYLTRANSFEREASE CENTER
Function / homology
Function and homology information


transferase activity / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome
Similarity search - Function
SH3 type barrels. - #30 / Nucleic acid-binding proteins / Ribosomal protein L2, bacterial/organellar-type / SH3 type barrels. / Ribosomal protein L2 signature. / Ribosomal protein L2, conserved site / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein L2, domain 3 / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal ...SH3 type barrels. - #30 / Nucleic acid-binding proteins / Ribosomal protein L2, bacterial/organellar-type / SH3 type barrels. / Ribosomal protein L2 signature. / Ribosomal protein L2, conserved site / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein L2, domain 3 / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Roll / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Large ribosomal subunit protein uL2
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsNakagawa, A. / Hosaka, H. / Nakashima, T. / Tanaka, I.
Citation
Journal: EMBO J. / Year: 1999
Title: The three-dimensional structure of the RNA-binding domain of ribosomal protein L2; a protein at the peptidyl transferase center of the ribosome.
Authors: Nakagawa, A. / Nakashima, T. / Taniguchi, M. / Hosaka, H. / Kimura, M. / Tanaka, I.
#1: Journal: J.Struct.Biol. / Year: 1998
Title: Crystallization and preliminary X-ray crystallographic study of a 23S rRNA binding domain of the ribosomal protein L2 from Bacillus stearothermophilus
Authors: Nakashima, T. / Kimura, M. / Nakagawa, A. / Tanaka, I.
History
DepositionMar 25, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (RIBOSOMAL PROTEIN L2)
B: PROTEIN (RIBOSOMAL PROTEIN L2)


Theoretical massNumber of molelcules
Total (without water)29,8622
Polymers29,8622
Non-polymers00
Water1,964109
1
A: PROTEIN (RIBOSOMAL PROTEIN L2)


Theoretical massNumber of molelcules
Total (without water)14,9311
Polymers14,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (RIBOSOMAL PROTEIN L2)


Theoretical massNumber of molelcules
Total (without water)14,9311
Polymers14,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.050, 36.190, 69.710
Angle α, β, γ (deg.)99.58, 95.86, 102.63
Int Tables number1
Cell settingtriclinic
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper: (Code: given
Matrix: (-0.999427, -0.006932, 0.033133), (-0.014974, 0.968367, -0.249082), (-0.030359, -0.249436, -0.967915)
Vector: -16.317, -18.993, 27.649)

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Components

#1: Protein PROTEIN (RIBOSOMAL PROTEIN L2)


Mass: 14930.819 Da / Num. of mol.: 2 / Mutation: METHIONINES ARE SUBSTITUED BY SELONOMETHIONINE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: PET-22B / Gene (production host): L2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)LYSS / References: UniProt: P04257
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.18 Å3/Da / Density % sol: 43 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 15% PEK20000 IN 0.1M MES PH6, pH 6.5
Components of the solutions
IDNameCrystal-IDSol-ID
1PEK2000011
2MES11
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlprotein1drop
210 mMTris-HCl1drop
31 mMdithiothreitol1drop
410-15 %(w/w)PEG200001reservoir
50.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.9000, 0.9785, 0.9788
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 15, 1998 / Details: FOCUSING MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97851
30.97881
ReflectionResolution: 2.3→40 Å / Num. obs: 11430 / % possible obs: 98.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.1 / % possible all: 96.8
Reflection
*PLUS
Num. measured all: 45101
Reflection shell
*PLUS
% possible obs: 96.8 %

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Processing

Software
NameVersionClassification
SHARPphasing
SOLOMONphasing
CNS0.5refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1117 9.8 %RANDOM
Rwork0.203 ---
all-11415 --
obs-11415 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.4 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.11 Å24.4 Å2-2.89 Å2
2--12.94 Å2-5.8 Å2
3----8.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 0 0 109 2173
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.03
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.21.5
X-RAY DIFFRACTIONx_mcangle_it3.472
X-RAY DIFFRACTIONx_scbond_it3.572
X-RAY DIFFRACTIONx_scangle_it4.872.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight Biso : 0.2 / Weight position: 5

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)
11RESTRAINTS0.0940.369
220.0990.331
330.1310.289
440.0870.221
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 184 9.9 %
Rwork0.258 1668 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Rfactor obs: 0.258

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