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- PDB-1dcr: CRYSTAL STRUCTURE OF DNA SHEARED TANDEM G-A BASE PAIRS -

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Basic information

Entry
Database: PDB / ID: 1dcr
TitleCRYSTAL STRUCTURE OF DNA SHEARED TANDEM G-A BASE PAIRS
Components5'-D(*CP*CP*GP*AP*AP*(BRU)P*GP*AP*GP*G)-3'
KeywordsDNA / TANDEM GA BASE PAIRS / GA MISMATCH / DEOXYRIBONUCLEIC ACID
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGao, Y.-G. / Robinson, H. / Sanishvili, R. / Joachimiak, A. / Wang, A.H.-J.
CitationJournal: Biochemistry / Year: 1999
Title: Structure and recognition of sheared tandem G x A base pairs associated with human centromere DNA sequence at atomic resolution.
Authors: Gao, Y.G. / Robinson, H. / Sanishvili, R. / Joachimiak, A. / Wang, A.H.
History
DepositionNov 5, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 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_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_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_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.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_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: 5'-D(*CP*CP*GP*AP*AP*(BRU)P*GP*AP*GP*G)-3'
B: 5'-D(*CP*CP*GP*AP*AP*(BRU)P*GP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6167
Polymers6,3182
Non-polymers2985
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)20.950, 61.860, 68.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-23-

MG

21A-1042-

HOH

31B-1024-

HOH

41B-1070-

HOH

51B-1090-

HOH

61B-1091-

HOH

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Components

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


Mass: 3158.913 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1.76 Å3/Da / Density % sol: 29.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MPD, MGCL2, TRIS, SPERMINE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1SPERMINE11
2MGCL211
3TRIS11
4MPD11
5MPD12
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.3 mMDNA duplex1drop
22 mMTris-HCl1drop
35 mM1dropMgCl2
52.6 %1drop
640 %MPD1reservoir
41

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 17, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 5771 / Num. obs: 5771 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.61 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 19.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 3.8 / % possible all: 93.7
Reflection
*PLUS
% possible obs: 85.1 % / Observed criterion σ(F): 1

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
d*TREKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB STRUCTURE 1D9R

1d9r


Resolution: 1.6→20 Å / Num. parameters: 2055 / Num. restraintsaints: 1837 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: PARKINSON ET AL. / Details: SHELX-97 OPTIONS HOPE
RfactorNum. reflection% reflectionSelection details
Rfree0.266 291 5 %RANDOM
all0.196 5771 --
obs0.191 5409 98.4 %-
Solvent computationSolvent model: SHELX-97 OPTIONS SWAT
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 412 34 77 523
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.067
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.072
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.066
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.192 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS

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