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- PDB-1pjg: RNA/DNA Hybrid Decamer of CAAAGAAAAG/CTTTTCTTTG -

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Basic information

Entry
Database: PDB / ID: 1pjg
TitleRNA/DNA Hybrid Decamer of CAAAGAAAAG/CTTTTCTTTG
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: 1.15 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 2, 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_alt_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)6,4076
Polymers6,2472
Non-polymers1604
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.701, 41.073, 46.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.93 Å3/Da / Density % sol: 36.38 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: calcium acetate, cacodylate, beta-octylglucoside, spermidine hydrochloride, 2-methyl,2,4-pentanediol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Components of the solutions
IDNameCrystal-IDSol-ID
1calcium acetate11
2cacodylate11
3beta-octylglucoside11
4spermidine HCl11
52-methyl,2,4-pentanediol11
6calcium acetate12
72-methyl,2,4-pentanediol12
Crystal grow
*PLUS
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
740 %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: 1.15→50 Å / Num. obs: 17368 / % possible obs: 96.2 % / Observed criterion σ(I): 4.7 / Biso Wilson estimate: 8.17 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 29.6
Reflection shellResolution: 1.15→1.18 Å / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 11.09 / Num. unique all: 882 / % possible all: 93.9
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 96 %
Reflection shell
*PLUS
% possible obs: 93.9 %

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Processing

Software
NameVersionClassification
ADSCQuantum 4data collection
SCALEPACKdata scaling
EPMRphasing
SHELXL-97refinement
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ID AH0001

Resolution: 1.15→8 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.163 871 5 %random
Rwork0.132 ---
all-16497 --
obs-16497 95.1 %-
Displacement parametersBiso mean: 10.71 Å2
Refine analyzeOccupancy sum hydrogen: 1 / Occupancy sum non hydrogen: 1
Refinement stepCycle: LAST / Resolution: 1.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 414 4 124 542
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_bond_d0.009
LS refinement shellResolution: 1.15→1.18 Å /
Rfactor% reflection
Rwork0.132 -
obs-93.9 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.158 / Rfactor Rwork: 0.127
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.028

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