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

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Basic information

Entry
Database: PDB / ID: 3bns
TitleCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (A1555G mutant, Br-derivative)
Components
  • (A site of human mitochondrial ribosome, chain three) x 2
  • A site of human mitochondrial ribosome, chain two
KeywordsRNA / ribosome / decoding site
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Feb 21, 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_conn_type / 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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id / _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
A: A site of human mitochondrial ribosome, chain three
B: A site of human mitochondrial ribosome, chain two
C: A site of human mitochondrial ribosome, chain three
D: A site of human mitochondrial ribosome, chain three
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7376
Polymers28,6594
Non-polymers782
Water1,838102
1
A: A site of human mitochondrial ribosome, chain three
B: A site of human mitochondrial ribosome, chain two
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5213
Polymers14,4822
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: A site of human mitochondrial ribosome, chain three
D: A site of human mitochondrial ribosome, chain three
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2153
Polymers14,1762
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.670, 77.120, 56.490
Angle α, β, γ (deg.)90.000, 115.680, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-43-

HOH

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Components

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


Mass: 7394.280 Da / Num. of mol.: 2 / Mutation: A1555G / Source method: obtained synthetically
#2: RNA chain A site of human mitochondrial ribosome, chain two


Mass: 7088.115 Da / Num. of mol.: 1 / Mutation: A1555G / Source method: obtained synthetically
#3: RNA chain A site of human mitochondrial ribosome, chain three


Mass: 6781.949 Da / Num. of mol.: 1 / Mutation: A1555G / Source method: obtained synthetically
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium cacodylate, KCl, spermine tetrachloride, tobramycin, 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: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→35.39 Å / Num. obs: 21598 / % possible obs: 97.4 % / Redundancy: 3.76 % / Rmerge(I) obs: 0.031 / Χ2: 0.98 / Net I/σ(I): 16.2 / Scaling rejects: 614
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.9-1.973.810.3782.8819221501.2897.4
1.97-2.053.790.3013.4807621321.297.6
2.05-2.143.810.2384.1822121571.1597.6
2.14-2.253.810.1825.1825621651.0797.9
2.25-2.393.790.127.1826621770.9398.4
2.39-2.583.790.0869.5830421830.8798.4
2.58-2.843.770.05514.2830921840.7698.8
2.84-3.253.770.02925.2831321820.7398.4
3.25-4.093.690.02638.2814021670.8496.6
4.09-35.393.570.01856.4773621011.0192.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→35.39 Å / FOM work R set: 0.771 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.26 2146 9.7 %
Rwork0.247 --
obs-21594 97.4 %
Solvent computationBsol: 68.542 Å2
Displacement parametersBiso mean: 49.315 Å2
Baniso -1Baniso -2Baniso -3
1--8.096 Å20 Å2-6.907 Å2
2--10.56 Å20 Å2
3----2.464 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1892 2 102 1996
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.818
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1rna_free.paramrna_free.top
X-RAY DIFFRACTION2bru.parambru.top
X-RAY DIFFRACTION3par2_xplor.parampar2_xplor.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top

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