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

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Basic information

Entry
Database: PDB / ID: 3bno
TitleCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (Br-derivative)
ComponentsA site of human mitochondrial ribosome
KeywordsRNA / ribosome / decoding site
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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 / 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

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Assembly

Deposited unit
A: A site of human mitochondrial ribosome
B: A site of human mitochondrial ribosome
C: A site of human mitochondrial ribosome
D: A site of human mitochondrial ribosome


Theoretical massNumber of molelcules
Total (without water)27,0644
Polymers27,0644
Non-polymers00
Water55831
1
A: A site of human mitochondrial ribosome
B: A site of human mitochondrial ribosome


Theoretical massNumber of molelcules
Total (without water)13,5322
Polymers13,5322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: A site of human mitochondrial ribosome
D: A site of human mitochondrial ribosome


Theoretical massNumber of molelcules
Total (without water)13,5322
Polymers13,5322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.140, 45.460, 52.130
Angle α, β, γ (deg.)71.430, 73.420, 74.050
Int Tables number1
Space group name H-MP1

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Components

#1: RNA chain
A site of human mitochondrial ribosome


Mass: 6765.949 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.74 Å3/Da / Density % sol: 55.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium cacodylate, spermine tetrachloride, paromomycin, KCl, 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: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.35→36.88 Å / Num. obs: 11751 / % possible obs: 97.8 % / Redundancy: 3.93 % / Rmerge(I) obs: 0.038 / Χ2: 0.99 / Net I/σ(I): 17.8 / Scaling rejects: 695
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.35-2.433.970.3663.2908722850.9697.7
2.43-2.533.950.2873.9936723680.9498.3
2.53-2.653.940.2254.6917223230.9298.1
2.65-2.793.950.1516.4934123610.9198.3
2.79-2.963.920.0949.1937223840.8899
2.96-3.193.920.04616.1936523730.8998.4
3.19-3.513.920.03922.2934723570.9998.6
3.51-4.023.940.03528.2931923401.0198.5
4.02-5.063.960.03140.8955123821.1698.5
5.06-36.883.820.02945.9869122101.2992.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→36.88 Å / FOM work R set: 0.688 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.255 1204 10.1 %
Rwork0.226 --
obs-11718 98.1 %
Solvent computationBsol: 74.988 Å2
Displacement parametersBiso mean: 67.94 Å2
Baniso -1Baniso -2Baniso -3
1--7.529 Å221.764 Å2-11.173 Å2
2--4.792 Å20.604 Å2
3---2.736 Å2
Refinement stepCycle: LAST / Resolution: 2.35→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1788 0 31 1819
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.901
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1rna_free.paramrna_free.top
X-RAY DIFFRACTION2bru.parambru.top
X-RAY DIFFRACTION3CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top

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