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- PDB-1dfu: CRYSTAL STRUCTURE OF E.COLI RIBOSOMAL PROTEIN L25 COMPLEXED WITH ... -

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Basic information

Entry
Database: PDB / ID: 1dfu
TitleCRYSTAL STRUCTURE OF E.COLI RIBOSOMAL PROTEIN L25 COMPLEXED WITH A 5S RRNA FRAGMENT AT 1.8 A RESOLUTION
Components
  • (5S RRNA5S ribosomal RNA) x 2
  • RIBOSOMAL PROTEIN L25
KeywordsRIBOSOME / PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


response to radiation / ribosomal large subunit assembly / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / structural constituent of ribosome / translation / cytosol / cytoplasm
Similarity search - Function
Ribosomal Protein L25; Chain P / Ribosomal Protein L25; Chain P / Ribosomal protein L25, short-form / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsLu, M. / Steitz, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution.
Authors: Lu, M. / Steitz, T.A.
History
DepositionNov 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
M: 5S RRNA
N: 5S RRNA
P: RIBOSOMAL PROTEIN L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1978
Polymers23,0763
Non-polymers1225
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.6, 76.6, 95.1
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: RNA chain 5S RRNA / 5S ribosomal RNA


Mass: 6155.753 Da / Num. of mol.: 1 / Fragment: LOOP E-HELIX IV FRAGMENT / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN E.COLI
#2: RNA chain 5S RRNA / 5S ribosomal RNA


Mass: 6206.706 Da / Num. of mol.: 1 / Fragment: LOOP E-HELIX IV FRAGMENT / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN E.COLI
#3: Protein RIBOSOMAL PROTEIN L25 /


Mass: 10713.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PROTEIN FROM THE LARGE RIBOSOMAL SUBUNIT / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PL25 / Production host: Escherichia coli (E. coli) / References: UniProt: P68919
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MPD, POTASSIUM CHLORIDE, MAGNESIUM CHLORIDE, CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP at 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCL11
2MGCL211
3CACODYLATECacodylic acid11
4MPD11
5MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlRNA-complex1drop
220 %MPD1drop
350 mMNa cacodylate1drop
4100 mM1dropKCl
510 mM1dropMgCl2
620 %(v/v)MPD1reservoir
70.4 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 24727 / % possible obs: 96 % / Observed criterion σ(I): 2.9 / Redundancy: 15 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 11
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5 % / Rmerge(I) obs: 0.313 / % possible all: 77
Reflection shell
*PLUS
% possible obs: 77 % / Mean I/σ(I) obs: 2.9

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(I): 2 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2164 10 %RANDOM
Rwork0.207 ---
all0.209 25857 --
obs0.226 21705 83.9 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms753 819 5 242 1819
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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