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- PDB-2fqn: Crystal structure of the Homo sapiens cytoplasmic ribosomal decod... -

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Basic information

Entry
Database: PDB / ID: 2fqn
TitleCrystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site
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 / RNA duplex / rRNA / Decoding site / A site / Homo sapiens cytoplasm
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKondo, J. / Urzhumtsev, A. / Westhof, E.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site.
Authors: Kondo, J. / Urzhumtsev, A. / Westhof, E.
History
DepositionJan 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_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)15,2437
Polymers14,7112
Non-polymers5325
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.050, 47.390, 56.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-347-

HOH

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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-MG / MAGNESIUM ION


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


Mass: 161.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM sodium cacodylate, 5 mM hexammine cobalt, 200 mM Potassium chloride, 1% (v/v) 2-methyl-2,4-pentanediol , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2hexammine cobalt11
3Potassium chloride11
42-methyl-2,4-pentanediol11
5H2O11
6sodium cacodylate12
7hexammine cobalt12
8Potassium chloride12
9H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 2004
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→28.55 Å / Num. obs: 4878 / % possible obs: 83.1 % / Redundancy: 3.33 % / Rmerge(I) obs: 0.117 / Χ2: 0.95 / Net I/σ(I): 7.2 / Scaling rejects: 123
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 78.5 % / Redundancy: 2.39 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2 / Num. measured all: 1048 / Num. unique obs: 438 / Χ2: 0.34

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata processing
CNSrefinement
PDB_EXTRACT1.701data extraction
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→10 Å / FOM work R set: 0.799 / σ(F): 3
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
Rfree0.282 410 7.1 %RANDOM
Rwork0.247 ---
obs-3976 68.8 %-
Solvent computationBsol: 56.064 Å2
Displacement parametersBiso mean: 40.951 Å2
Baniso -1Baniso -2Baniso -3
1--2.108 Å20 Å20 Å2
2---5.402 Å20 Å2
3---7.51 Å2
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 918 35 51 1004
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d1.8
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
2.3-2.40.322210.306246267
2.4-2.530.334370.326369406
2.53-2.680.356520.322408460
2.68-2.890.362530.34469522
2.89-3.170.336660.273510576
3.17-3.610.279610.231519580
3.61-4.480.251580.202506564
4.48-100.225620.222539601
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION2nco_xplor.param
X-RAY DIFFRACTION3mo6_xplor.param
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param

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