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- PDB-1qa6: CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1qa6
TitleCRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX
Components
  • 58 NUCLEOTIDE RIBOSOMAL RNA DOMAIN
  • RIBOSOMAL PROTEIN L11
KeywordsRIBOSOME / RIBOSOMAL RNA / TERTIARY STRUCTUR / E RNA-PROTEIN INTERACTION / MINOR GROOVE BINDING / ANTIBIOTIC BINDING
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex
Similarity search - Function
Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily ...Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
OSMIUM ION / RNA / RNA (> 10) / Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsConn, G.L. / Draper, D.E. / Lattman, E.E. / Gittis, A.G.
CitationJournal: Science / Year: 1999
Title: Crystal structure of a conserved ribosomal protein-RNA complex.
Authors: Conn, G.L. / Draper, D.E. / Lattman, E.E. / Gittis, A.G.
History
DepositionApr 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
C: 58 NUCLEOTIDE RIBOSOMAL RNA DOMAIN
D: 58 NUCLEOTIDE RIBOSOMAL RNA DOMAIN
A: RIBOSOMAL PROTEIN L11
B: RIBOSOMAL PROTEIN L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,54112
Polymers51,6834
Non-polymers8588
Water00
1
C: 58 NUCLEOTIDE RIBOSOMAL RNA DOMAIN
A: RIBOSOMAL PROTEIN L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2716
Polymers25,8422
Non-polymers4294
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 58 NUCLEOTIDE RIBOSOMAL RNA DOMAIN
B: RIBOSOMAL PROTEIN L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2716
Polymers25,8422
Non-polymers4294
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.675, 150.675, 63.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.043157, -0.998994, -0.012207), (-0.392208, -0.005704, -0.919859), (0.918863, 0.044486, -0.39206)
Vector: 166.83, 180.4792, -58.8074)

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Components

#1: RNA chain 58 NUCLEOTIDE RIBOSOMAL RNA DOMAIN


Mass: 18725.191 Da / Num. of mol.: 2 / Fragment: NTS 1051-1108 FROM E. COLI 23S RRNA / Mutation: U1061A / Source method: obtained synthetically
Details: RNA SYNTHESIZED BY IN VITRO TRANSCRIPTION USING T7 RNA POLYMERASE
#2: Protein RIBOSOMAL PROTEIN L11


Mass: 7116.356 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: PET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P56210
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-OS / OSMIUM ION


Mass: 190.230 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Os

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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: 3.5 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 600, MAGNESIUM ACETATE, COBALT HEXAMINE CHLORIDE, SODIUM CACODYLATE, KCL, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 310.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1MAGNESIUM ACETATE11
2[CO(NH3)6]CL311
3KCL11
4CACODYLATE11
5PEG 60011
6PEG 60012
Crystal grow
*PLUS
Temperature: 37 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMsodium cacodylate1reservoir
215 %PEG6001reservoir
380 mM1reservoirMg(OAc)2
4100 mM1reservoirKCl
50.2 mM1reservoirCo(NH3)6Cl3
61

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.13951
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13951 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 17542 / Num. obs: 17542 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 75.5 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 23.3
Reflection shellResolution: 2.8→2.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.27 / % possible all: 88.7
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Redundancy: 5 % / Num. measured all: 89078 / Biso Wilson estimate: 75.5 Å2
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.93 Å / % possible obs: 88.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.9

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.321 1324 7.3 %RANDOM
Rwork0.24 ---
all0.25 16757 --
obs0.24 16757 94.5 %-
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 2486 8 0 3482
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg2.64
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→2.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 50 5.7 %
Rwork0.42 688 -
obs--84.4 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Rfactor obs: 0.24 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_improper_angle_d / Dev ideal: 4.118
LS refinement shell
*PLUS
Rfactor Rfree: 0.36 / Rfactor Rwork: 0.42

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