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

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Basic information

Entry
Database: PDB / ID: 3bnt
TitleCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the Presence of [Co(NH3)6]Cl3 (A1555G mutant, Br-derivative)
ComponentsA site of human mitochondrial ribosome
KeywordsRNA / ribosome / decoding site
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 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 1.2Sep 27, 2017Group: Data collection / Category: pdbx_diffrn_reflns_shell / Item: _pdbx_diffrn_reflns_shell.percent_possible_obs
Revision 2.0Feb 21, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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Assembly

Deposited unit
A: A site of human mitochondrial ribosome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2713
Polymers7,0871
Non-polymers1842
Water97354
1
A: A site of human mitochondrial ribosome
hetero molecules

A: A site of human mitochondrial ribosome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5426
Polymers14,1742
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area4330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.865, 74.865, 22.537
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-78-

HOH

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Components

#1: RNA chain A site of human mitochondrial ribosome


Mass: 7087.131 Da / Num. of mol.: 1 / Mutation: A1555G / Source method: obtained synthetically
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium cacodylate, KCl, spermine tetrachloride, paromomycin, 2-methyl-2,4-pentanediol, hexammine cobalt chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2KCl11
3Sodium cacodylate11
4[Co(NH3)6]Cl311
5MPD12
6KCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.91950, 0.91984, 0.91637
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91951
20.919841
30.916371
ReflectionRedundancy: 9.9 % / Av σ(I) over netI: 5.1 / Number: 33495 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / D res high: 2.301 Å / D res low: 37.406 Å / Num. obs: 3368 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.2737.4199.410.070.078.3
5.147.2799.910.0560.0569
4.25.1410010.0650.0659.3
3.644.210010.0790.0799.7
3.253.6410010.0760.0769.9
2.973.2510010.0810.0819.9
2.752.9710010.0950.09510.1
2.572.7510010.1460.14610.3
2.422.5710010.2330.23310.5
2.32.4210010.3040.30410.5
ReflectionResolution: 2.3→37.432 Å / Num. obs: 3374 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.4210.50.2632.449214700.263100
2.42-2.5710.40.1813.547944630.181100
2.57-2.7510.20.1164.843934310.116100
2.75-2.97100.0856.540334040.085100
2.97-3.259.90.07637893820.07100
3.25-3.649.90.0657.832693310.065100
3.64-4.29.70.0727.729313020.072100
4.2-5.149.40.0598.524422610.059100
5.14-7.2790.0479.618972100.047100
7.27-37.438.30.0529.39961200.05297.2

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.91643.8-5.25
13 wavelength20.91954.01-6.68
13 wavelength30.91993.85-7.51

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Processing

Software
NameVersionClassificationNB
SCALAdata processing
SOLVE2.12phasing
CNSrefinement
PDB_EXTRACT3.004data extraction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→37.432 Å / FOM work R set: 0.768 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.255 335 9.9 %
Rwork0.217 --
obs-3368 99.9 %
Solvent computationBsol: 43.732 Å2
Displacement parametersBiso mean: 34.779 Å2
Baniso -1Baniso -2Baniso -3
1--0.608 Å2-1.671 Å20 Å2
2---0.608 Å20 Å2
3---1.215 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 464 8 54 526
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION2bru.parambru.top
X-RAY DIFFRACTION3nco_xplor.paramnco_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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