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- PDB-1wqz: Complicated water orientations in the minor groove of B-DNA decam... -

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Basic information

Entry
Database: PDB / ID: 1wqz
TitleComplicated water orientations in the minor groove of B-DNA decamer D(CCATTAATGG)2 observed by neutron diffraction measurements
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
Biological speciessynthetic construct (others)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 3 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 1.3Mar 7, 2018Group: Data collection / Category: diffrn_detector
Item: _diffrn_detector.details / _diffrn_detector.detector / _diffrn_detector.type
Revision 1.4Jul 4, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / pdbx_entity_src_syn
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.5Oct 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
Water48627
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 / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 2

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Sample preparation

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: 279 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: JRR-3M / Beamline: 1G-A / Wavelength: 2.6 Å
DetectorDetector: IMAGE PLATE / Date: May 17, 2003 / Details: JAERI BIX-4
RadiationMonochromator: ELASTICALLY-BENT PERFECT SILICON MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.6 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. all: 1420 / Num. obs: 896 / % possible obs: 63.1 % / Redundancy: 1.23 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.233 / Net I/σ(I): 5.803
Reflection shellResolution: 3→3.18 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 3.633 / Num. unique all: 213 / % possible all: 62.4

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WQY

1wqy


Resolution: 3→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 79 5.7 %RANDOM
Rwork0.252 ---
obs0.252 879 63.4 %-
all-1386 --
Displacement parametersBiso mean: 7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.13 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 27 431
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONc_bond_d0.026
NEUTRON DIFFRACTIONc_angle_deg1.06
NEUTRON DIFFRACTIONc_dihedral_angle_d0
NEUTRON DIFFRACTIONc_improper_angle_d1.16
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.345 8 5.26 %
Rwork0.333 100 -
obs--65.8 %

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