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- PDB-265d: STRUCTURAL STUDIES ON NUCLEIC ACIDS -

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Basic information

Entry
Database: PDB / ID: 265d
TitleSTRUCTURAL STUDIES ON NUCLEIC ACIDS
ComponentsDNA (5'-D(*CP*GP*(5CM)P*GP*AP*AP*TP*TP*(5CM)P*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.01 Å
AuthorsPartridge, B.L. / Salisbury, S.A.
Citation
#1: Journal: Thesis, University of Cambridge / Year: 1996
Title: Structural Studies on Nucleic Acids
Authors: Partridge, B.L.
History
DepositionJul 12, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Aug 28, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Other
Revision 1.4Feb 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_conn_type / 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.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.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.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_type.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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,4073
Polymers7,3832
Non-polymers241
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.426, 40.490, 65.319
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*(5CM)P*GP*AP*AP*TP*TP*(5CM)P*GP*CP*G)-3')


Mass: 3691.446 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growpH: 7.1 / Details: pH 7.10
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA CACODYLATE11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 15, 1995
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.01→32.6 Å / Num. obs: 11473 / Rmerge(I) obs: 0.1148

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Processing

Software
NameClassification
NUCLSQrefinement
RIGAKUdata reduction
RIGAKUdata scaling
RefinementMethod to determine structure: MIR / Highest resolution: 2.01 Å / σ(F): 4
Details: STANDARD R-FACTOR = 17.2% ERROR R-FACTOR = 5.3% WEIGHTED R-FACTOR = 16.8% NUMBER OF REFLECTIONS INCLUDED = 11473 AVERAGE |FO-FC| DISCREPANCY = 29.47 AVERAGE WEIGHTED |FO-FC| DISCREPANCY = 0. ...Details: STANDARD R-FACTOR = 17.2% ERROR R-FACTOR = 5.3% WEIGHTED R-FACTOR = 16.8% NUMBER OF REFLECTIONS INCLUDED = 11473 AVERAGE |FO-FC| DISCREPANCY = 29.47 AVERAGE WEIGHTED |FO-FC| DISCREPANCY = 0.13 CORRELATION COEFFICIENT = 102.8% RESOLUTION BREAKDOWN "ALL" R FACTOR = 17.2%
RfactorNum. reflection% reflection
obs0.172 4233 86.2 %
Refinement stepCycle: LAST / Highest resolution: 2.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 490 1 117 608
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d0.0240.015
X-RAY DIFFRACTIONn_angle_d0.0530.025
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it10.027.5
X-RAY DIFFRACTIONn_sugar_angle_it11.0087.5
X-RAY DIFFRACTIONn_phos_bond_it10.7077.5
X-RAY DIFFRACTIONn_phos_angle_it11.2297.5
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d0.0280.015
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0570.025
X-RAY DIFFRACTIONn_plane_restr0.0290.015
X-RAY DIFFRACTIONn_chiral_restr0.0550.04
X-RAY DIFFRACTIONn_singtor_nbd0.1010.063
X-RAY DIFFRACTIONn_multtor_nbd0.2720.063
X-RAY DIFFRACTIONn_xhyhbond_nbd0.3930.063

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