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- PDB-3opi: 7-DEAZA-2'-DEOXYADENOSINE modification in B-FORM DNA -

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Basic information

Entry
Database: PDB / ID: 3opi
Title7-DEAZA-2'-DEOXYADENOSINE modification in B-FORM DNA
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*(7DA)P*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DODECAMER / 7-DEAZA-DEOXYADENOSINE / 7-DEAZA-DA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsKowal, E.A. / Ganguly, M. / Pallan, P.S. / Marky, L.A. / Gold, B. / Egli, M. / Stone, M.P.
CitationJournal: J.Phys.Chem.B / Year: 2011
Title: Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2'-deoxyadenosine:dT Base Pairing in DNA.
Authors: Kowal, E.A. / Ganguly, M. / Pallan, P.S. / Marky, L.A. / Gold, B. / Egli, M. / Stone, M.P.
History
DepositionSep 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.value / _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.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_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

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*AP*(7DA)P*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*(7DA)P*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4417
Polymers7,3252
Non-polymers1165
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-30 kcal/mol
Surface area4150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.635, 40.310, 65.928
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: DNA chain DNA (5'-D(*CP*GP*CP*GP*AP*(7DA)P*TP*TP*CP*GP*CP*G)-3')


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: DROPLETS CONTAINING 0.6 MM OLIGONUCLEOTIDE, 5% 2-METHYL-2,4-PENTANEDIOL (MPD), 20 MM SODIUM CACODYLATE, 6 MM SPERMINE TETRAHYDROCHLORIDE, 40 MM NACL WERE EQUILIBRATED AGAINST A RESERVOIR OF ...Details: DROPLETS CONTAINING 0.6 MM OLIGONUCLEOTIDE, 5% 2-METHYL-2,4-PENTANEDIOL (MPD), 20 MM SODIUM CACODYLATE, 6 MM SPERMINE TETRAHYDROCHLORIDE, 40 MM NACL WERE EQUILIBRATED AGAINST A RESERVOIR OF 0.75 ML OF 35% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. all: 28548 / Num. obs: 27920 / % possible obs: 97.8 % / Observed criterion σ(I): 165.4 / Redundancy: 10.6 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 61.3
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.39 / Num. unique all: 2679 / % possible all: 95.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 355D

355d


Resolution: 1.1→34.4 Å
RfactorNum. reflectionSelection details
Rfree0.195 2162 RANDOM
Rwork0.161 --
all0.164 28548 -
obs-27920 -
Refinement stepCycle: LAST / Resolution: 1.1→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 5 133 624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.0236
X-RAY DIFFRACTIONo_angle_deg1.95
LS refinement shellResolution: 1.1→1.14 Å
RfactorNum. reflection% reflection
Rfree0.195 2162 -
Rwork0.161 --
obs-2679 97.9 %

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