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- PDB-1f69: CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE -

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Basic information

Entry
Database: PDB / ID: 1f69
TitleCRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE
ComponentsDNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
KeywordsDNA / B-DNA / E-DNA / DOUBLE HELIX
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT, REAL SPACE TRANSLATION/ROTATION/RIGID BODY SEARCH USING A CUSTOM X-PLOR 3.851 SCRIPT / Resolution: 2.6 Å
AuthorsVargason, J.M. / Eichman, B.F. / Ho, P.S.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: The extended and eccentric E-DNA structure induced by cytosine methylation or bromination.
Authors: Vargason, J.M. / Eichman, B.F. / Ho, P.S.
History
DepositionJun 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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_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.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.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.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_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(*GP*GP*CP*GP*CP*C)-3')
B: DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8064
Polymers3,6202
Non-polymers1852
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.590, 42.590, 63.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Cell settingtetragonal
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-14-

NCO

21A-15-

HOH

31B-21-

HOH

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Components

#1: DNA chain DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')


Mass: 1810.205 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-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.: 18 / 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: 3.76 Å3/Da / Density % sol: 67.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MGCL2, CO(NH3)6, SPERMINE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MGCL211
2CO(NH3)611
3SPERMINE11
4SODIUM CACODYLATE11
5MGCL212
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.7 mMDNA1drop
225 mMsodium cacodylate1drop
30.8 mM1dropMgCl2
40.75 mMspermine-tetrahydrochloride1drop
515 %(v/v)MPD1reservoir
625 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→500 Å / Num. all: 2026 / Num. obs: 2026 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 27
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.251 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 20150
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
d*TREKdata reduction
d*TREKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, REAL SPACE TRANSLATION/ROTATION/RIGID BODY SEARCH USING A CUSTOM X-PLOR 3.851 SCRIPT
Resolution: 2.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: PARKINSON ET AL.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 214 11 %RANDOM
Rwork0.205 ---
all0.2136 1938 --
obs0.2134 1937 --
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 10 12 262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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