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- PDB-1evv: CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RE... -

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Basic information

Entry
Database: PDB / ID: 1evv
TitleCRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTION
ComponentsPHENYLALANINE TRANSFER RNA
KeywordsRNA / TRANSFER RNA / PHENYLALANINE / PHE-TRNA / YEAST / AMINO-ACID TRANSPORT
Function / homologySPERMINE / : / RNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsJovine, L. / Djordjevic, S. / Rhodes, D.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The crystal structure of yeast phenylalanine tRNA at 2.0 A resolution: cleavage by Mg(2+) in 15-year old crystals.
Authors: Jovine, L. / Djordjevic, S. / Rhodes, D.
#1: Journal: J.Mol.Biol. / Year: 1972
Title: High-resolution X-ray diffraction studies on a pure species of transfer RNA
Authors: Ladner, J.E. / Finch, J.T. / Klug, A. / Clark, B.F.
#2: Journal: Nature / Year: 1974
Title: Structure of yeast phenylalanine tRNA at 3 A resolution
Authors: Robertus, J.D. / Ladner, J.E. / Finch, J.T. / Rhodes, D. / Brown, R.S. / Clark, B.F.C. / Klug, A.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1975
Title: Structure of yeast phenylalanine transfer RNA at 2.5 A resolution
Authors: Ladner, J.E. / Jack, A. / Robertus, J.D. / Brown, R.S. / Rhodes, D. / Clark, B.F. / Klug, A.
#4: Journal: J.Mol.Biol. / Year: 1978
Title: Further refinement of the structure of yeast tRNA Phe
Authors: Hingerty, B. / Brown, R.S. / Jack, A.
#5: Journal: Biochemistry / Year: 1986
Title: Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles
Authors: Westhof, E. / Sundaralingam, M.
#6: Journal: Acta Crystallogr.,Sect.A / Year: 1988
Title: Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals
Authors: Westhof, E. / Dumas, P. / Moras, D.
History
DepositionApr 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_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: PHENYLALANINE TRANSFER RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,33612
Polymers24,8901
Non-polymers44511
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.252, 32.988, 61.882
Angle α, β, γ (deg.)90.00, 90.38, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: RNA chain PHENYLALANINE TRANSFER RNA


Mass: 24890.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces (fungus) / Genus: Saccharomyces / References: GenBank: 176479
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.25 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 277.15 K / Method: dialysis / pH: 7.5
Details: CRYSTALS GROWN AT 277 K IN 0.010 M TRIS-HCL PH 7.5, 0.012 M MGCL2, 0.002 M SPERMINE, 6% 1,6-HEXANEDIOL. CRYOPROTECTION CONDITIONS: AFTER WASHING IN FRESH CRYSTALLIZATION SOLUTION FOR 10 MIN ...Details: CRYSTALS GROWN AT 277 K IN 0.010 M TRIS-HCL PH 7.5, 0.012 M MGCL2, 0.002 M SPERMINE, 6% 1,6-HEXANEDIOL. CRYOPROTECTION CONDITIONS: AFTER WASHING IN FRESH CRYSTALLIZATION SOLUTION FOR 10 MIN AND ADDITION OF 30% MPD (V/V), CRYSTALS WERE FLASH-FROZEN IN LIQUID NITROGEN, DIALYSIS, temperature 277.15K
Components of the solutions
IDNameCrystal-IDSol-ID
1TRIS-HCLTris11
2MGCL211
3SPERMINE11
41,6-HEXANEDIOL11
5MGCL212
61,6-HEXANEDIOL12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mltRNA1
210 mMTris-HCl12
312 mM12MgCl2
42 mMspermine12
56 %(v/v)1,6-hexanediol1
61

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.932
DetectorType: ADSC / Detector: CCD / Date: Apr 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 2→25.8 Å / Num. all: 13678 / Num. obs: 13678 / % possible obs: 88.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 29.3 Å2 / Rsym value: 0.036 / Net I/σ(I): 14.8
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.171 / % possible all: 70.7
Reflection
*PLUS
Num. measured all: 30638 / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 70.7 % / Rmerge(I) obs: 0.171

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSphasing
RefinementStarting model: PDB ENTRY 1TRA
Resolution: 2→25.79 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 810557.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: PARKINSON ET AL.
Details: A LOW RESOLUTION LIMIT OF 6.O A WAS USED FOR INITIAL B FACTOR AND BULK SOLVENT CORRECTIONS. THE OCCUPANCY OF NUCLEOTIDE D16, AS WELL AS THOSE OF ATOMS P, O1P, O2P, O5* AND C5* OF NUCLEOTIDE ...Details: A LOW RESOLUTION LIMIT OF 6.O A WAS USED FOR INITIAL B FACTOR AND BULK SOLVENT CORRECTIONS. THE OCCUPANCY OF NUCLEOTIDE D16, AS WELL AS THOSE OF ATOMS P, O1P, O2P, O5* AND C5* OF NUCLEOTIDE D17, WERE REFINED TO ACCOUNT FOR MG2+-CATALYSED PARTIAL CLEAVAGE OF THE TRNA BACKBONE AT EITHER SIDE OF D16. DENSITY FOR THIS PART OF THE MOLECULE WAS POOR AND ITS PLACEMENT SHOULD THEREFORE BE CONSIDERED TENTATIVE. OCCUPANCIES OF ALL MG2+ IONS, THE SPERMINE AND ALL WATER MOLECULES WERE ALSO REFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 926 6.8 %RANDOM
Rwork0.227 ---
all0.227 13678 --
obs0.227 13678 88.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 113.1 Å2 / ksol: 0.468 e/Å3
Displacement parametersBiso mean: 53.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å20 Å23.76 Å2
2---0.56 Å20 Å2
3----1.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2→25.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1652 24 220 1896
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d12.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.3
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.11 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.38 101 6.6 %
Rwork0.324 1432 -
obs--70.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1TRNA_RNA.PARAMTRNA_RNA.TOP
X-RAY DIFFRACTION2TRNA_ION.PARAMTRNA_ION.TOP
X-RAY DIFFRACTION3TRNA_LIGAND.PARAMTRNA_LIGAND.TOP
X-RAY DIFFRACTION4WATER_REP.PARAWATER.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg12.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.413 / Rfactor Rwork: 0.34

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