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- PDB-398d: 3'-DNA-RNA-5' JUNCTION FORMED DURING INITIATION OF MINUS-STRAND S... -

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Basic information

Entry
Database: PDB / ID: 398d
Title3'-DNA-RNA-5' JUNCTION FORMED DURING INITIATION OF MINUS-STRAND SYNTHESIS OF HIV REPLICATION
Components
  • DNA/RNA (5'-R(*GP*CP*CP*AP)-D(*CP*TP*GP*C)-3')
  • RNA (5'-R(*GP*CP*AP*GP*UP*GP*GP*C)-3')
KeywordsDNA-RNA HYBRID / A-DNA/RNA / DOUBLE HELIX
Function / homologyDNA/RNA hybrid / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.94 Å
AuthorsMueller, U. / Meier, G. / Mochi-Onori, A. / Cellai, L. / Heumann, H.
CitationJournal: Biochemistry / Year: 1998
Title: Crystal structure of an eight-base pair duplex containing the 3'-DNA-RNA-5' junction formed during initiation of minus-strand synthesis of HIV replication.
Authors: Mueller, U. / Maier, G. / Mochi Onori, A. / Cellai, L. / Heumann, H. / Heinemann, U.
History
DepositionMay 4, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 6, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*CP*AP*GP*UP*GP*GP*C)-3')
B: DNA/RNA (5'-R(*GP*CP*CP*AP)-D(*CP*TP*GP*C)-3')
C: RNA (5'-R(*GP*CP*AP*GP*UP*GP*GP*C)-3')
D: DNA/RNA (5'-R(*GP*CP*CP*AP)-D(*CP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)10,0664
Polymers10,0664
Non-polymers00
Water1,51384
1
A: RNA (5'-R(*GP*CP*AP*GP*UP*GP*GP*C)-3')
B: DNA/RNA (5'-R(*GP*CP*CP*AP)-D(*CP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,0332
Polymers5,0332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*GP*CP*AP*GP*UP*GP*GP*C)-3')
D: DNA/RNA (5'-R(*GP*CP*CP*AP)-D(*CP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,0332
Polymers5,0332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.740, 44.150, 51.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 2581.601 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA/RNA hybrid DNA/RNA (5'-R(*GP*CP*CP*AP)-D(*CP*TP*GP*C)-3')


Mass: 2451.580 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2KCL11
3SPERMINE11
4SODIUM CACODYLATE11
5MPD11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.25 mMhybrid duplex1drop
220 mMsodium cacodylate1drop
36 mMspermine tetrahydrochloride1drop
410 mM1dropKCl
55 %1drop
635 %MPD1reservoir
71

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONEMBL/DESY, HAMBURG BW7A1
SYNCHROTRONEMBL/DESY, HAMBURG X312
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATENov 28, 1997
MARRESEARCH2IMAGE PLATENov 28, 1997
Radiation
IDScattering typeWavelength-ID
1x-ray1
2x-ray2
Radiation wavelength
IDRelative weight
11
21
ReflectionResolution: 1.94→15 Å / Num. obs: 7612 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 24.44 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.4
Reflection shellResolution: 1.94→2.04 Å / Redundancy: 3 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.2 / % possible all: 93.1
Reflection
*PLUS
Highest resolution: 1.94 Å / Lowest resolution: 15 Å / % possible obs: 99.2 %
Reflection shell
*PLUS
Lowest resolution: 1.96 Å / % possible obs: 93.1 %

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Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: CANONICAL A-RNA MODEL OF IDENTICAL SIZE AND SEQUENCE

Resolution: 1.94→15 Å / Cross valid method: RANDOM IN THIN SHELLS / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.291 405 5 %RANDOM IN THIN SHELLS
Rwork0.22 ---
obs0.22 7566 99.2 %-
Displacement parametersBiso mean: 24.01 Å2
Refinement stepCycle: LAST / Resolution: 1.94→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 666 0 84 750
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.701
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.94→2.03 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.398 54 5 %
Rwork0.303 823 -
Xplor fileSerial no: 1 / Param file: DNA-RNA-MULTI-ENDO.PARAM / Topol file: DNA-RNA-MULTI-ENDO.TOP
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.94 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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