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- PDB-1pjo: Crystal Structure of an RNA/DNA hybrid of HIV-1 PPT -

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Basic information

Entry
Database: PDB / ID: 1pjo
TitleCrystal Structure of an RNA/DNA hybrid of HIV-1 PPT
Components
  • 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3'
  • 5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'
KeywordsDNA-RNA HYBRID / RNA/DNA hybrid / Polypurine Tract of HIV-1 / Moleuclar Replacement / sugar conformation / DNA-RNA COMPLEX
Function / homologyDNA / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsKopka, M.L. / Lavelle, L. / Han, G.W. / Ng, H.-L. / Dickerson, R.E.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: An Unusual Sugar Conformation in the Structure of an RNA/DNA Decamer of the Polypurine Tract May Affect Recognition by RNase H
Authors: Kopka, M.L. / Lavelle, L. / Han, G.W. / Ng, H.-L. / Dickerson, R.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Direct Methods Determination of an RNA/DNA Hybrid Decamer at 1.15A Resolution
Authors: Han, G.W.
#2: Journal: To be Published / Year: 2003
Title: Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation: Dimer Formation by Base-pair Swapping
Authors: Han, G.W. / Kopka, M.L. / Langs, D. / Sawaya, M.R. / Dickerson, R.E.
History
DepositionJun 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: 5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'
B: 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3938
Polymers6,2472
Non-polymers1466
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.595, 40.755, 45.740
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 5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'


Mass: 3255.076 Da / Num. of mol.: 1 / Fragment: Polypurine Tract of HIV-1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3'


Mass: 2991.961 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 1.89 Å3/Da / Density % sol: 35.09 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: magnesium acetate, beta-octylglucoside, spermidine hydrochloride, cacodylate, 2-methyl,2,4-pentanediol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Components of the solutions
IDNameCrystal-IDSol-ID
1magensium acetate11
2cacodylate11
3beta-octylglucoside11
4spermidine HCl11
52-methyl,2,4-pentanediol11
6magensium acetate12
72-methyl,2,4-pentanediol12
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.3 mMhybrid duplex1drop
212 mMcalcium acetate1drop
30.6 mMspermidine hydrochloride1droppH6.8
40.075 %beta-octyl-glycoside1drop
512 mMsodium cacodylate1droppH6.8
612 %(v/v)MPD1drop
750 %MPD1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 1999 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. all: 18877 / Num. obs: 18327 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.058 / Net I/σ(I): 33.7
Reflection shellResolution: 1.1→1.13 Å / % possible obs: 74.6 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 4.06 / % possible all: 74.6
Reflection
*PLUS
Lowest resolution: 20 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ID AH0001

Resolution: 1.1→20 Å / Num. parameters: 5231 / Num. restraintsaints: 19473 / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1564 918 5 %Random
Rwork0.1166 ---
all0.117 17409 --
obs-17409 --
Displacement parametersBiso mean: 13.76 Å2
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 700 35 99 834
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONs_angle_d0.0430.017
X-RAY DIFFRACTIONs_bond_d0.0190.011
LS refinement shellResolution: 1.1→1.13 Å / Rfactor Rwork: 0.492
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.156 / Rfactor Rwork: 0.117
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONs_bond_d0.03
X-RAY DIFFRACTIONs_angle_d0.06

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