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- PDB-267d: STRUCTURAL STUDIES ON NUCLEIC ACIDS -

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Basic information

Entry
Database: PDB / ID: 267d
TitleSTRUCTURAL STUDIES ON NUCLEIC ACIDS
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5CM)P*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED / COMPLEXED WITH DRUG
Function / homologyDISTAMYCIN A / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,8614
Polymers7,3552
Non-polymers5062
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.918, 40.141, 66.306
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*AP*TP*TP*(5CM)P*GP*CP*G)-3')


Mass: 3677.419 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-DMY / DISTAMYCIN A / DISTAMYCIN / STALLIMYCIN


Mass: 481.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N9O4 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
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: May 13, 1995
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→34.3 Å / Num. obs: 10301 / Rmerge(I) obs: 0.0742

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Processing

Software
NameClassification
NUCLSQrefinement
RIGAKUdata reduction
RIGAKUdata scaling
RefinementMethod to determine structure: MIR / Highest resolution: 2 Å / σ(F): 4
Details: STANDARD R-FACTOR = 15.6% ERROR R-FACTOR = 5.5% WEIGHTED R-FACTOR = 13.7% NUMBER OF REFLECTIONS INCLUDED = 10301 AVERAGE |FO-FC| DISCREPANCY = 20.38 AVERAGE WEIGHTED |FO-FC| DISCREPANCY = 0. ...Details: STANDARD R-FACTOR = 15.6% ERROR R-FACTOR = 5.5% WEIGHTED R-FACTOR = 13.7% NUMBER OF REFLECTIONS INCLUDED = 10301 AVERAGE |FO-FC| DISCREPANCY = 20.38 AVERAGE WEIGHTED |FO-FC| DISCREPANCY = 0.10 CORRELATION COEFFICIENT = 99.2% RESOLUTION BREAKDOWN "ALL" R FACTOR = 14.7%
RfactorNum. reflection% reflection
obs0.156 3703 76.4 %
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 488 36 74 598
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it12.6327.5
X-RAY DIFFRACTIONn_sugar_angle_it13.7597.5
X-RAY DIFFRACTIONn_phos_bond_it13.7597.5
X-RAY DIFFRACTIONn_phos_angle_it13.8777.5
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_d0.0290.015
X-RAY DIFFRACTIONn_phos_bond_angle_d
X-RAY DIFFRACTIONn_plane_restr0.0340.015
X-RAY DIFFRACTIONn_chiral_restr0.0540.04
X-RAY DIFFRACTIONn_singtor_nbd0.2220.063
X-RAY DIFFRACTIONn_multtor_nbd0.220.063
X-RAY DIFFRACTIONn_xhyhbond_nbd

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