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- PDB-307d: Structure of a DNA analog of the primer for HIV-1 RT second stran... -

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Basic information

Entry
Database: PDB / ID: 307d
TitleStructure of a DNA analog of the primer for HIV-1 RT second strand synthesis
Components
  • DNA (5'-D(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
  • DNA (5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MIR PHASE ANALYSIS / Resolution: 1.85 Å
AuthorsHan, G.W. / Kopka, M.L. / Cascio, D. / Grzeskowiak, K. / Dickerson, R.E.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis.
Authors: Han, G.W. / Kopka, M.L. / Cascio, D. / Grzeskowiak, K. / Dickerson, R.E.
History
DepositionJan 7, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 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: DNA (5'-D(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
B: DNA (5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3')
C: DNA (5'-D(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
D: DNA (5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3')
E: DNA (5'-D(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
F: DNA (5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)18,2616
Polymers18,2616
Non-polymers00
Water2,486138
1
A: DNA (5'-D(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
B: DNA (5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,0872
Polymers6,0872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
D: DNA (5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,0872
Polymers6,0872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DNA (5'-D(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
F: DNA (5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,0872
Polymers6,0872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.820, 28.280, 72.490
Angle α, β, γ (deg.)90.00, 103.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain DNA (5'-D(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')


Mass: 3095.083 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3')


Mass: 2991.961 Da / Num. of mol.: 3 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 1.63 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MG ACETATE11
4SPERMIDINE11
5BETA-OCTAGLUCOSIDE11
6WATER12
7MPD12
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.17 mMDNA decamer1dropdouble helix
21.53 mMmagnesium acetate1drop
30.17 mMspermidine1drop
40.05 %(v/v)beta-octaglucoside1drop
59.5 %(v/v)MPD1drop
61
71

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: MIRROR MSC-YALE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. obs: 9686 / % possible obs: 93.8 % / Biso Wilson estimate: 24.6 Å2 / Rsym value: 0.058
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3 % / Mean I/σ(I) obs: 5 / Rsym value: 0.24 / % possible all: 91
Reflection
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 100 Å / % possible obs: 93.8 % / Rmerge(I) obs: 0.058

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Processing

Software
NameClassification
MLPHAREphasing
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR PHASE ANALYSIS
Starting model: IDEAL B-DNA HELIX OF SEQUENCE CAAAGAAAAG

Resolution: 1.85→8 Å / σ(F): 2
Details: THIS ENTRY PRESENTS THE COORDINATES OF THE CRYSTAL STRUCTURE OF CAAAGAAAAG AND ITS COMPLEMENTARY STRAND. THERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT. HOWEVER, THE FIRST MOLECULE (HELIX #1 ...Details: THIS ENTRY PRESENTS THE COORDINATES OF THE CRYSTAL STRUCTURE OF CAAAGAAAAG AND ITS COMPLEMENTARY STRAND. THERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT. HOWEVER, THE FIRST MOLECULE (HELIX #1 WITH STRANDS A AND B) IS ORDERED, AND THE SECOND MOLECULE IS DISORDERED WITH HELIX #2 (STRANDS C AND D) AND HELIX #3 (STRANDS E AND F). THIS IS EVIDENCED BY THE MULTIPLE ISOMORPHOUS REPLACEMENT METHOD FROM ONE BROMINE AND ONE IODINE ISOMORPHOUS DERIVATIVE PLUS ANOMALOUS DATA. HELICES IN THE SECOND MOLECULE ARE DISORDERED END-FOR-END WITH HALF-WEIGHT HELICES #2 AND #3 BEING RELATED BY A TWOFOLD AXIS THROUGH THEIR CENTERS, NORMAL TO THE HELICAL AXIS. THE OCCUPANCY FOR THE HELIX #2 IS 0.52 AND FOR THE HELIX #3 IS 0.46.
RfactorNum. reflection% reflection
obs0.233 9630 93 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1212 0 138 1350
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0150.45
X-RAY DIFFRACTIONt_angle_deg2.1341
X-RAY DIFFRACTIONt_dihedral_angle_d15.951
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.00710
X-RAY DIFFRACTIONt_it4.5
X-RAY DIFFRACTIONt_nbd0.01610
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor Rwork: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d15.95
X-RAY DIFFRACTIONt_plane_restr0.00710

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