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- PDB-1wqy: X-RAY structural analysis of B-DNA decamer D(CCATTAATGG)2 crystal... -

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Basic information

Entry
Database: PDB / ID: 1wqy
TitleX-RAY structural analysis of B-DNA decamer D(CCATTAATGG)2 crystal grown in D2O solution
Components5'-D(*CP*CP*AP*TP*TP*AP*AP*TP*GP*G)-3'
KeywordsDNA / B-DNA / HYDRATION / HYDROGEN
Function / homologyDEUTERATED WATER / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsArai, S. / Chatake, T. / Ohhara, T. / Kurihara, K. / Tanaka, I. / Suzuki, N. / Fujimoto, Z. / Mizuno, H. / Niimura, N.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements
Authors: Arai, S. / Chatake, T. / Ohhara, T. / Kurihara, K. / Tanaka, I. / Suzuki, N. / Fujimoto, Z. / Mizuno, H. / Niimura, N.
History
DepositionOct 7, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: 5'-D(*CP*CP*AP*TP*TP*AP*AP*TP*GP*G)-3'
B: 5'-D(*CP*CP*AP*TP*TP*AP*AP*TP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,0882
Polymers6,0882
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.900, 32.900, 96.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 3044.017 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: D2O

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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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 279 K / Method: batch (d2o) / pH: 7
Details: 30% MPD, 0.1M MAGNESIUM CHLORIDE, 0.1M SODIUM CACODYLATE, 0.002M DNA, pD 6.6, pH 7.0, BATCH (D2O), temperature 279K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2MgCl11
3SODIUM CACODYLATE11
4D2O11
5MPD12
6MgCl12
7D2O12

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.71 / Wavelength: 0.71 Å
DetectorDetector: IMAGE PLATE / Date: Jun 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 8528 / Num. obs: 8451 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 9.27 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.025
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.25 % / Rmerge(I) obs: 0.108 / Num. unique all: 828 / % possible all: 97.9

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 167D

167d


Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: LIMITING RESOLUTION ESTIMATED FROM DATA COLLECTION STATISTICS WAS 1.6 ANGSTROMS. HOWEVER, THE STRUCTURAL REFINEMENT PROCESSING WAS COMPUTED BY USING REFLECTIONS 2.0 - 50.0 ANGSTROMS BECAUSE ...Details: LIMITING RESOLUTION ESTIMATED FROM DATA COLLECTION STATISTICS WAS 1.6 ANGSTROMS. HOWEVER, THE STRUCTURAL REFINEMENT PROCESSING WAS COMPUTED BY USING REFLECTIONS 2.0 - 50.0 ANGSTROMS BECAUSE THE BIN R VALUE AND BIN FREE R VALUE OF RESOLUTION RANGE HIGHER THAN 2.0 ANGSTROMS WERE VERY HIGH.
RfactorNum. reflection% reflectionSelection details
Rfree0.284 474 -RANDOM
Rwork0.237 ---
obs0.237 4361 97.7 %-
all-4361 --
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 87 491
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d17.3
X-RAY DIFFRACTIONc_improper_angle_d1.45
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.048
RfactorNum. reflection% reflection
Rfree0.338 49 -
Rwork0.288 --
obs--98.5 %

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