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- PDB-1g00: ALTERNATION OF DNA AND SOLVENT LAYERS IN THE A FORM OF D(GGCGCC) ... -

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Basic information

Entry
Database: PDB / ID: 1g00
TitleALTERNATION OF DNA AND SOLVENT LAYERS IN THE A FORM OF D(GGCGCC) OBTAINED BY ETHANOL CRYSTALLIZATION
Components5'-D(*GP*GP*CP*GP*CP*C)-3'
KeywordsDNA / DOUBLE HELIX / A-DNA / DNA LAYERS
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsUrpi, L. / Navaza, J. / Subirana, J.A.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2000
Title: Alternation of DNA and solvent layers in the A form of d(GGCGCC) obtained by ethanol crystallization.
Authors: Urpi, L. / Navaza, J. / Subirana, J.A.
History
DepositionOct 5, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Feb 7, 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 1.6Apr 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(*GP*GP*CP*GP*CP*C)-3'
B: 5'-D(*GP*GP*CP*GP*CP*C)-3'
C: 5'-D(*GP*GP*CP*GP*CP*C)-3'
D: 5'-D(*GP*GP*CP*GP*CP*C)-3'
E: 5'-D(*GP*GP*CP*GP*CP*C)-3'
F: 5'-D(*GP*GP*CP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)10,8616
Polymers10,8616
Non-polymers00
Water23413
1
A: 5'-D(*GP*GP*CP*GP*CP*C)-3'
B: 5'-D(*GP*GP*CP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*GP*GP*CP*GP*CP*C)-3'
D: 5'-D(*GP*GP*CP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-D(*GP*GP*CP*GP*CP*C)-3'
F: 5'-D(*GP*GP*CP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.149, 36.900, 110.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-103-

HOH

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Components

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


Mass: 1810.205 Da / Num. of mol.: 6 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.05 Å3/Da / Density % sol: 39.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: ethanol, magnesium chloride, sodium cacodylate, tetra-arginine, spermine tetrachloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1ethanol11
2magnesium chloride11
3sodium cacodylate11
4tetra-arginine11
5spermine tetrachloride11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER / Date: Jul 14, 1988
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.297→55.015 Å / Num. all: 3504 / Num. obs: 3504 / % possible obs: 79 % / Observed criterion σ(F): 1 / Redundancy: 1 % / Rmerge(I) obs: 0.0525
Reflection shellResolution: 2.3→2.45 Å / Redundancy: 1 % / Rmerge(I) obs: 0.274 / Num. unique all: 456 / % possible all: 61.8

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
CAD4data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A-DNA form fiber

Resolution: 2.3→8 Å / Num. parameters: 2801 / Num. restraintsaints: 3093 / σ(I): 2
Stereochemistry target values: Clowney et al. Gelbin et al. Parkinson et al.
Details: Used Konnert-Hendrickson conjugate-gradient algorithm instead of the full matrix approach.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 168 -Every 20 reflections one was kept for R-free calculations
Rwork0.1875 ---
all0.2137 3376 --
obs0.205 2839 78.7 %-
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 687 0 13 700
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d1.1

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