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- PDB-1dpn: B-DODECAMER CGCGAA(TAF)TCGCG WITH INCORPORATED 2'-DEOXY-2'-FLUORO... -

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Basic information

Entry
Database: PDB / ID: 1dpn
TitleB-DODECAMER CGCGAA(TAF)TCGCG WITH INCORPORATED 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*(TAF)P*TP*CP*GP*CP*G)-3')
KeywordsDNA / 0.95 A RESOLUTION STRUCTURE
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.95 Å
AuthorsEgli, M. / Tereshko, V. / Teplova, M. / Minasov, G. / Joachimiak, A. / Sanishvili, R. / Weeks, C.M. / Miller, R. / Maier, M.A. / An, H. ...Egli, M. / Tereshko, V. / Teplova, M. / Minasov, G. / Joachimiak, A. / Sanishvili, R. / Weeks, C.M. / Miller, R. / Maier, M.A. / An, H. / Dan Cook, P. / Manoharan, M.
CitationJournal: Biopolymers / Year: 1998
Title: X-ray crystallographic analysis of the hydration of A- and B-form DNA at atomic resolution.
Authors: Egli, M. / Tereshko, V. / Teplova, M. / Minasov, G. / Joachimiak, A. / Sanishvili, R. / Weeks, C.M. / Miller, R. / Maier, M.A. / An, H. / Dan Cook, P. / Manoharan, M.
History
DepositionDec 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(TAF)P*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(TAF)P*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4606
Polymers7,3632
Non-polymers974
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.623, 39.732, 65.737
Angle α, β, γ (deg.)90.00, 90.00, 90.0
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 3681.383 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: SODIUM CACODYLATE, MAGNESIUM ACETATE, SPERMINE, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MAGNESIUM ACETATE11
3SPERMINE11
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.25 mMdecamer1dropsingle strand
220 mMsodium cacodylate1drop
36 mMspermine1drop
410 mM1dropMg2+
540 mM1dropK+
635 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.8152
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8152 Å / Relative weight: 1
ReflectionResolution: 0.95→20 Å / Num. all: 39151 / Num. obs: 39151 / % possible obs: 94.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.047
Reflection shellResolution: 0.95→1 Å / % possible all: 70.2
Reflection
*PLUS
Num. measured all: 291875

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 0.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: PARKINSON ET AL.
RfactorNum. reflection% reflectionSelection details
Rfree0.159 3900 10 %RANDOM
Rwork0.171 ---
all0.16 39151 --
obs0.16 39151 94.3 %-
Refinement stepCycle: LAST / Resolution: 0.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 570 4 252 826
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.005
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
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): 0 / % reflection Rfree: 10 % / Rfactor all: 0.16 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 0.95 Å / Lowest resolution: 1 Å / Num. reflection obs: 4082 / Rfactor obs: 0.306

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