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- PDB-3e9w: X-Ray Crystal Structure of the hexamer DCACACG:Crystal grown in t... -

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Basic information

Entry
Database: PDB / ID: 3e9w
TitleX-Ray Crystal Structure of the hexamer DCACACG:Crystal grown in the presence of cobalt(III)hexammine Chloride.
Components
  • 5'-D(*CP*AP*CP*AP*CP*G)-3'
  • 5'-D(*CP*GP*TP*GP*TP*G)-3'
KeywordsDNA / Z DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsVenkadesh, S. / Mandal, P.K. / Gautham, N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: The structure of d(CACACG).d(CGTGTG).
Authors: Venkadesh, S. / Mandal, P.K. / Gautham, N.
History
DepositionAug 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,6182
Polymers3,6182
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-7 kcal/mol
Surface area2350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.854, 43.440, 17.847
Angle α, β, γ (deg.)90.00, 119.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 1778.207 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*TP*GP*TP*G)-3'


Mass: 1840.227 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 1.67 Å3/Da
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.99
Details: cobalt(III)hexammine chloride,spermine and 50% MPD, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Components of the solutions
IDNameCrystal-IDSol-ID
1cobalt(III)hexammine chloride11
2spermine11
3MPD11
4cobalt(III)hexammine chloride12
5MPD12

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 30, 2006
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→15 Å / Num. all: 1384 / Num. obs: 1384 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.73 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 11.7
Reflection shellResolution: 2.05→2.13 Å / Redundancy: 2.74 % / Rmerge(I) obs: 0.1984 / Mean I/σ(I) obs: 2.5 / Num. unique all: 120 / % possible all: 94.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fiber model of Z-DNA

Resolution: 2.05→14.58 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU ML: 0.225 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26375 66 4.8 %RANDOM
Rwork0.23507 ---
obs0.23663 1314 92.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.975 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.03 Å2
2--0.05 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.05→14.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 0 20 260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0420.021268
X-RAY DIFFRACTIONr_angle_refined_deg6.4073410
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.02126
X-RAY DIFFRACTIONr_nbd_refined0.2960.2136
X-RAY DIFFRACTIONr_nbtor_refined0.4240.2139
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3450.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3980.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5820.25
LS refinement shellResolution: 2.05→2.107 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.706 2 -
Rwork0.527 80 -
obs--96.47 %

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