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

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Basic information

Entry
Database: PDB / ID: 3bnq
TitleCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SrCl2 (A1555G mutant, Br-derivative)
Components(A site of human mitochondrial ribosome, ...) x 2
KeywordsRNA / ribosome / decoding site
Function / homology: / PAROMOMYCIN / STRONTIUM ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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, A chain
B: A site of human mitochondrial ribosome, A chain
C: A site of human mitochondrial ribosome, A chain
D: A site of human mitochondrial ribosome, B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,36015
Polymers28,9654
Non-polymers1,39511
Water2,396133
1
A: A site of human mitochondrial ribosome, A chain
B: A site of human mitochondrial ribosome, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0916
Polymers14,7892
Non-polymers3024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: A site of human mitochondrial ribosome, A chain
D: A site of human mitochondrial ribosome, B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2699
Polymers14,1762
Non-polymers1,0937
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.266, 76.056, 55.912
Angle α, β, γ (deg.)90.000, 117.060, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

SR

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Components

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A site of human mitochondrial ribosome, ... , 2 types, 4 molecules ABCD

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


Mass: 7394.280 Da / Num. of mol.: 3 / Mutation: A1555G / Source method: obtained synthetically
#2: RNA chain A site of human mitochondrial ribosome, B chain


Mass: 6781.949 Da / Num. of mol.: 1 / Mutation: A1555G / Source method: obtained synthetically

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Non-polymers , 4 types, 144 molecules

#3: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Sr
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium cacodylate, KCl, spermine tetrachloride, paromomycin, 2-methyl-2,4-pentanediol, SrCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2KCl11
3Sodium cacodylate11
4SrCl211
5MPD12
6KCl12
7SrCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.92070, 0.92110, 0.91625
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 20, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.92071
20.92111
30.916251
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 7 / Number: 60538 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / D res high: 2 Å / D res low: 49.662 Å / Num. obs: 17465 / % possible obs: 97.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.3249.6696.410.050.053.3
4.476.3299.410.0460.0463.3
3.654.4799.710.0460.0463.6
3.163.6510010.0340.0343.6
2.833.1699.910.0360.0363.7
2.582.8310010.0560.0563.7
2.392.5810010.0860.0863.7
2.242.3910010.130.133.7
2.112.2497.810.2080.2083.4
22.1185.610.280.282.6
ReflectionResolution: 2→49.791 Å / Num. obs: 17519 / % possible obs: 97.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.112.60.3731.9567822070.37385.5
2.11-2.243.30.2752.5811324280.27597.9
2.24-2.393.70.1684863923180.168100
2.39-2.583.70.1086.3807121740.108100
2.58-2.833.70.06210.8743720060.062100
2.83-3.163.70.03911668018130.03999.9
3.16-3.653.60.03612582516000.036100
3.65-4.473.60.04710.9485213570.04799.6
4.47-6.323.30.04611348010530.04699.4
6.32-49.793.40.04411.619195630.04496.2

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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 wavelength10.91626.14-9.8
13 wavelength20.92076.84-6.98
13 wavelength30.92112.24-9.63

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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→49.791 Å / FOM work R set: 0.795 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.269 1728 9.6 %
Rwork0.229 --
obs-17514 97.2 %
Solvent computationBsol: 65.271 Å2
Displacement parametersBiso mean: 47.179 Å2
Baniso -1Baniso -2Baniso -3
1-0.467 Å20 Å2-5.31 Å2
2--2.062 Å20 Å2
3----2.528 Å2
Refinement stepCycle: LAST / Resolution: 2→49.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1912 52 133 2097
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_d0.0041.5
X-RAY DIFFRACTIONc_angle_deg0.82
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1rna_free.param
X-RAY DIFFRACTION2bru.param
X-RAY DIFFRACTION3par2_xplor.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION6srO_xplor.param

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