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- PDB-3bnp: Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Dec... -

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Basic information

Entry
Database: PDB / ID: 3bnp
TitleCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (A1555G Mutant)
Components
  • A site of human mitochondrial ribosome, A chain
  • A site of human mitochondrial ribosome, B chain
KeywordsRNA / ribosome / decoding site
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsKondo, J. / Westhof, E.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates
Authors: Kondo, J. / Westhof, E.
History
DepositionDec 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A site of human mitochondrial ribosome, A chain
B: A site of human mitochondrial ribosome, B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7803
Polymers13,7412
Non-polymers391
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.350, 66.350, 57.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-27-

HOH

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Components

#1: RNA chain A site of human mitochondrial ribosome, A chain


Mass: 7023.250 Da / Num. of mol.: 1 / Mutation: A1555G / Source method: obtained synthetically
#2: RNA chain A site of human mitochondrial ribosome, B chain


Mass: 6718.068 Da / Num. of mol.: 1 / Mutation: A1555G / Source method: obtained synthetically
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium cacodylate, KCl, glycerol, paromomycin, 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2KCl11
3Sodium cacodylate11
4MPD12
5KCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9801 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.7→40.59 Å / Num. obs: 4215 / % possible obs: 99.5 % / Redundancy: 9.94 % / Rmerge(I) obs: 0.065 / Χ2: 0.99 / Net I/σ(I): 22 / Scaling rejects: 317
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.7-2.810.240.3623.943434240.51100
2.8-2.9110.290.2285.941484030.54100
2.91-3.0410.230.1458.743494250.61100
3.04-3.210.210.09613.642614150.78100
3.2-3.410.070.081841754120.93100
3.4-3.6610.120.0872042754161.03100
3.66-4.039.920.07725.942924251.22100
4.03-4.629.920.06834.143124311.45100
4.62-5.819.650.04944.742244331.4100
5.81-40.598.850.04648.138564311.5294.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→40.59 Å / FOM work R set: 0.775 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.27 433 10.2 %
Rwork0.231 --
obs-4204 99.3 %
Solvent computationBsol: 68.858 Å2
Displacement parametersBiso mean: 77.503 Å2
Baniso -1Baniso -2Baniso -3
1--8.62 Å2-13.852 Å20 Å2
2---8.62 Å20 Å2
3---17.241 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 908 1 13 922
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0051.5
X-RAY DIFFRACTIONc_angle_deg12
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1rna_free.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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