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- PDB-117d: CRYSTAL AND MOLECULAR STRUCTURE OF THE ALTERNATING DODECAMER D(GC... -

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Basic information

Entry
Database: PDB / ID: 117d
TitleCRYSTAL AND MOLECULAR STRUCTURE OF THE ALTERNATING DODECAMER D(GCGTACGTACGC) IN THE A-DNA FORM: COMPARISON WITH THE ISOMORPHOUS NON-ALTERNATING DODECAMER D(CCGTACGTACGG)
ComponentsDNA (5'-D(*GP*CP*GP*TP*AP*CP*GP*TP*AP*CP*GP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.55 Å
AuthorsBingman, C.A. / Jain, S. / Zon, G. / Sundaralingam, M.
Citation
Journal: Nucleic Acids Res. / Year: 1992
Title: Crystal and molecular structure of the alternating dodecamer d(GCGTACGTACGC) in the A-DNA form: comparison with the isomorphous non-alternating dodecamer d(CCGTACGTACGG).
Authors: Bingman, C.A. / Jain, S. / Zon, G. / Sundaralingam, M.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystal and Molecular Structure of the A-DNA Dodecamer d(CCGTACGTACGG): Choice of Fragment Helical Axis
Authors: Bingman, C.A. / Zon, G. / Sundaralingam, M.
History
DepositionFeb 10, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 22, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*GP*TP*AP*CP*GP*TP*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)3,6631
Polymers3,6631
Non-polymers00
Water59433
1
A: DNA (5'-D(*GP*CP*GP*TP*AP*CP*GP*TP*AP*CP*GP*C)-3')

A: DNA (5'-D(*GP*CP*GP*TP*AP*CP*GP*TP*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Unit cell
Length a, b, c (Å)46.200, 46.200, 71.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 3663.392 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2SPERMINE11
3[CO(NH3)6]3+11
4NA CACODYLATE11
5WATER12
6PROPANOL12
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMDNA duplex1drop
21 mMspermine1drop
33 mMcobalt hexammine1drop
430 %1-propanol1reservoir
51
61

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-6
DetectorDetector: OSCILLATION CAMERA
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.55 Å / Num. all: 2008 / Num. obs: 1115 / Observed criterion σ(I): 2
Reflection
*PLUS
Num. measured all: 2008 / Rmerge(I) obs: 0.05

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.55→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.142 1089
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.55→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 243 0 33 276
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_it2.43
X-RAY DIFFRACTIONn_sugar_angle_it3.34.5
X-RAY DIFFRACTIONn_phos_bond_it3.13
X-RAY DIFFRACTIONn_phos_angle_it3.94.5
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0060.025
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.020.05
X-RAY DIFFRACTIONn_phos_bond_d0.0240.05
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0450.075
X-RAY DIFFRACTIONn_plane_restr0.0150.04
X-RAY DIFFRACTIONn_chiral_restr0.0480.1
X-RAY DIFFRACTIONn_singtor_nbd0.1460.09
X-RAY DIFFRACTIONn_multtor_nbd0.1110.09
X-RAY DIFFRACTIONn_xhyhbond_nbd

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