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- PDB-1fir: CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTION PRIMER TRNA(LYS3) -

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Basic information

Entry
Database: PDB / ID: 1fir
TitleCRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTION PRIMER TRNA(LYS3)
ComponentsHIV-1 REVERSE TRANSCRIPTION PRIMER TRNA(LYS3)
KeywordsRNA / mammalian transfert ribonucleic acid / HIV-1 primer tRNA / amino acid transport / canonical tRNA structure / canonical anticodon / frameshifting / codon/anticodon mimicry / modified bases
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsBenas, P. / Dumas, P.
Citation
Journal: RNA / Year: 2000
Title: The crystal structure of HIV reverse-transcription primer tRNA(Lys,3) shows a canonical anticodon loop.
Authors: Benas, P. / Bec, G. / Keith, G. / Marquet, R. / Ehresmann, C. / Ehresmann, B. / Dumas, P.
#1: Journal: To be Published / Year: 2000
Title: Molecular blocs in tRNAs that could prevent +1 frameshifting
Authors: Benas, P. / Dumas, P.
#2: Journal: Thesis / Year: 2000
Title: Studies on the ternary initiation complex of HIV-1 reverse transcription and crystallographic structures of two partners
Authors: Benas, P.
History
DepositionAug 6, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 9, 2014Group: Derived calculations
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.6Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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

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Assembly

Deposited unit
A: HIV-1 REVERSE TRANSCRIPTION PRIMER TRNA(LYS3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8943
Polymers24,8471
Non-polymers472
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.72, 100.72, 82.61
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Cell settingtrigonal
Space group name H-MP3212

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Components

#1: RNA chain HIV-1 REVERSE TRANSCRIPTION PRIMER TRNA(LYS3)


Mass: 24847.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS, BOVINES AND CHICKENS
Source: (natural) Bos taurus (cattle)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 5.12 Å3/Da / Density % sol: 78.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 50 mM MES-KOH pH 5.6, 1.6 to 1.8 M Li2SO4, 10 mM MgCl2, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Li2SO411
2MgCl211
3MES-KOH11
4Li2SO412
5MgCl212
6MES-KOH12
Crystal
*PLUS
Density % sol: 78.7 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
250 mMMES/KOH1reservoir
310 mM1reservoirMgCl2
41.6-1.8 M1reservoirLi2SO4
51
61

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.9805
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9805 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. all: 6482 / Num. obs: 6482 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.081 / Net I/σ(I): 10.5
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 503 / Rsym value: 0.165 / % possible all: 71.6
Reflection
*PLUS
Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 71.6 % / Rmerge(I) obs: 0.165

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TNA

4tna


Resolution: 3.3→40 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 836049.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
Stereochemistry target values: modified CNS libraries (Parkinson et al.)
Details: R and free R improved by 12% and 11% respectively by a proper mask definition (see primary ref.)
RfactorNum. reflection% reflectionSelection details
Rfree0.227 543 9.2 %RANDOM
Rwork0.181 ---
obs0.181 5890 80.5 %-
all-6481 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.19 Å2 / ksol: 0.03 e/Å3
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.53 Å27.03 Å20 Å2
2--4.53 Å20 Å2
3----9.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 3.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1645 2 16 1663
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d2.06
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 34 4.9 %
Rwork0.221 666 -
obs--58.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA-REP-RESIPARAM.BPDNA-RNA-RESITOP.BP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 3 / % reflection Rfree: 9.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.06
LS refinement shell
*PLUS
Rfactor Rfree: 0.234 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.221

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