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- PDB-1d9r: CRYSTAL STRUCTURE OF DNA SHEARED TANDEM G-A BASE PAIRS -

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Basic information

Entry
Database: PDB / ID: 1d9r
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 / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD PHASING BY BROMINES / Resolution: 1.5 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 29, 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 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn / Item: _software.name / _struct_conn.pdbx_leaving_atom_flag
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 / 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 / _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.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

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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)6,4793
Polymers6,3182
Non-polymers1611
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.711, 67.216, 72.504
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
11A-21-

NCO

21A-1117-

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-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MPD, COBALT HEXAMMINE, MGCL2, TRIS, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1[CO(NH3)6]CL311
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
45 mM1dropCo(NH3)6+3
52.6 %1drop
640 %MPD1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9611
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 16, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9611 Å / Relative weight: 1
ReflectionResolution: 1.5→10 Å / Num. all: 8923 / Num. obs: 8923 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 33.7
Reflection shellResolution: 1.5→1.56 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.377 / % possible all: 100
Reflection
*PLUS

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD PHASING BY BROMINES / Resolution: 1.5→10 Å / Num. parameters: 2220 / Num. restraintsaints: 1837 / Cross valid method: A POSTERIORI / σ(F): 0 / σ(I): 0
Stereochemistry target values: G.PARKINSON, J.VOJTECHOVSKY, L.CLOWNEY, A.T.BRUNGER, H.M.BERMAN
Details: SHELXL HOPE OPTION
RfactorNum. reflection% reflectionSelection details
Rfree0.278 437 5 %RANDOM
Rwork0.234 ---
all0.234 8923 --
obs0.234 8923 99.9 %-
Solvent computationSolvent model: SHELXL SWAT OPTION
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 412 9 133 554
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.052
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.003
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.072
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.98
X-RAY DIFFRACTIONs_plane_restr0.052

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