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- PDB-1d8x: CRYSTAL STRUCTURE OF DNA SHEARED TANDEM G A BASE PAIRS -

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Basic information

Entry
Database: PDB / ID: 1d8x
TitleCRYSTAL STRUCTURE OF DNA SHEARED TANDEM G A BASE PAIRS
Components5'-D(*CP*CP*GP*AP*AP*TP*GP*AP*GP*G)-3'
KeywordsDNA / TANDEM GA BASE PAIRS / GA MISMATCH
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.2 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
DepositionOct 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 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 1.4Feb 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_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.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.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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,3985
Polymers6,1882
Non-polymers2103
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.784, 35.685, 22.466
Angle α, β, γ (deg.)90.00, 104.38, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-100-

HOH

21A-101-

HOH

31A-211-

HOH

41B-219-

HOH

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Components

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


Mass: 3094.042 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 1.83 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: MPD, COBALT HEXAMMINE, MGCL2, TRIS, pH 7.5, VAPOR DIFFUSION, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1COBALT HEXAMMINE11
2MGCL211
3TRIS11
4MPD11
5MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.3 mMDNA duplex1drop
22 mMTris-HCl1drop
35 mM1dropMgCl2
45 mM1drop[Co(NH3)6]3+
52.6 %1drop
615 %MPD1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. all: 12550 / Num. obs: 12550 / % possible obs: 81.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.5
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 1.25 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.7 / % possible all: 46.8
Reflection
*PLUS
Observed criterion σ(F): 1

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Processing

Software
NameVersionClassification
X-PLORmodel building
SHELXL-97refinement
d*TREKV. 5.1data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→20 Å / Num. parameters: 4386 / Num. restraintsaints: 5330 / Cross valid method: A POSTERIORI / σ(F): 0
Stereochemistry target values: G.PARKINSON, J.VOJTECHOVSKY, L.CLOWNEY, A.T.BRUNGER, H.M.BERMAN
RfactorNum. reflection% reflectionSelection details
Rfree0.246 633 5 %RANDOM
all0.188 12550 --
obs0.188 -81.7 %-
Solvent computationSolvent model: SHELXL SWAT OPTION
Refine analyzeNum. disordered residues: 0
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 412 19 128 559
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.073
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.044
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 11236 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.182 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

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