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- PDB-2g5k: Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decod... -

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Basic information

Entry
Database: PDB / ID: 2g5k
TitleCrystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with Apramycin
Components5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3'
KeywordsRNA / aminoglycoside / antibiotics / apramycin / ribosome / decoding site / Homo sapiens / cytoplasm
Function / homologyAPRAMYCIN / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKondo, J. / Francois, B. / Urzhumtsev, A. / Westhof, E.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2006
Title: Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site Complexed with Apramycin
Authors: Kondo, J. / Francois, B. / Urzhumtsev, A. / Westhof, E.
History
DepositionFeb 23, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_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: 5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3'
B: 5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1618
Polymers14,7112
Non-polymers1,4506
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.123, 33.123, 116.421
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: RNA chain 5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3'


Mass: 7355.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#2: Chemical ChemComp-AM2 / APRAMYCIN / NEBRAMYCIN II / 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE


Mass: 539.577 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H41N5O11
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 50mM sodium cacodylate, 10mM hexammine cobalt chloride, 150mM potassium chloride, 1%(v/v) 2-methyl-2,4-pentanediol, 5%(v/v) glycerol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2hexammine cobalt chloride11
3potassium chloride11
42-methyl-2,4-pentanediol11
5glycerol11
6H2O11
7sodium cacodylate12
8hexammine cobalt chloride12
9potassium chloride12
10glycerol12
11H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 18, 2003
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→27.85 Å / Num. obs: 3533 / % possible obs: 100 % / Redundancy: 5.59 % / Rmerge(I) obs: 0.056 / Χ2: 0.97 / Net I/σ(I): 16.8 / Scaling rejects: 151
Reflection shell

% possible obs: 100 %

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsΧ2
2.8-2.95.760.3972.119933460.35
2.9-3.025.760.3092.721903800.42
3.02-3.155.740.1515.118723260.53
3.15-3.325.780.1317.521213670.67
3.32-3.535.740.10310.119183340.82
3.53-3.85.730.08713.420923640.93
3.8-4.185.560.06321.120243611.17
4.18-4.785.430.05428.519423541.34
4.78-6.015.370.04338.318493371.61
6.01-27.855.010.03845.518863642.08

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata processing
CNSrefinement
PDB_EXTRACT1.701data extraction
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→10 Å / FOM work R set: 0.722 / σ(F): 0
Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996).
RfactorNum. reflection% reflectionSelection details
Rfree0.27 347 10.1 %RANDOM
Rwork0.258 ---
obs-3437 100 %-
Solvent computationBsol: 75.808 Å2
Displacement parametersBiso mean: 93.873 Å2
Baniso -1Baniso -2Baniso -3
1-7.932 Å2-1.148 Å20 Å2
2--7.932 Å20 Å2
3----15.865 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 938 102 15 1055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_improper_angle_d1.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.8-2.920.578340.553389423
2.92-3.070.51490.426378427
3.07-3.260.284490.155387436
3.26-3.50.302540.258369423
3.5-3.840.256410.282399440
3.84-4.350.308380.258386424
4.35-5.340.19460.234390436
5.34-100.273360.239392428
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION2am2_xplor.paramam2_xplor.top
X-RAY DIFFRACTION3nco_xplor.paramnco_xplor.top
X-RAY DIFFRACTION4mo6_xplor.parammo6_xplor.top
X-RAY DIFFRACTION5water_rep.paramwater.top

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