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- PDB-423d: 5'-D(*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)-3' -

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Basic information

Entry
Database: PDB / ID: 423d
Title5'-D(*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)-3'
ComponentsDNA (5'-D(*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)-3')
KeywordsDNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRozenberg, H. / Rabinovich, D. / Frolow, F. / Hegde, R.S. / Shakked, Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets.
Authors: Rozenberg, H. / Rabinovich, D. / Frolow, F. / Hegde, R.S. / Shakked, Z.
History
DepositionSep 14, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 14, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_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: DNA (5'-D(*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)-3')
B: DNA (5'-D(*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4487
Polymers7,3272
Non-polymers1225
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.067, 64.067, 44.679
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingtrigonal
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-133-

HOH

21A-150-

HOH

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Components

#1: DNA chain DNA (5'-D(*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)-3')


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.228 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1MGCL211
2SPERMINE11
3NA CACODYLATE11
4MPD11
5NA CACODYLATE12
6MPD12
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.8 mg/mlDNA1drop
270-80 mM1dropMgCl2
31
41-2 mMspermine tetrachloride1drop
520 mMsodium cacodylate1drop
66 %(w/v)1drop
723 %MPD1reservoir
8100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 3, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER, GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→23.6 Å / Num. all: 8888 / Num. obs: 8888 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 50.8
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 1.95 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 4.9 / % possible all: 95
Reflection
*PLUS
Observed criterion σ(F): 2 / Num. measured all: 68426
Reflection shell
*PLUS
% possible obs: 95 % / Num. unique obs: 8888

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Processing

Software
NameClassification
ULTIMAmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
ULTIMAphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IDEAL B-DNA

Resolution: 1.6→23.6 Å / Num. parameters: 2703 / Num. restraintsaints: 11946 / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.206 506 5.7 %RANDOM SELECTION
Rwork0.173 ---
all0.174 8888 --
obs0.173 8888 98.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER: J.MOL.BIOL. 91, 201-228 (1973)
Refine analyzeOccupancy sum non hydrogen: 644.67
Refinement stepCycle: LAST / Resolution: 1.6→23.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 35 127 648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0.024
X-RAY DIFFRACTIONs_from_restr_planes0.008
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.008
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / Rfactor obs: 0.174 / Lowest resolution: 23.6 Å / % reflection Rfree: 5.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_angle_deg

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