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- PDB-371d: STRUCTURAL VARIABILITY OF A-DNA IN CRYSTALS OF THE OCTAMER D(PCPC... -

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Basic information

Entry
Database: PDB / ID: 371d
TitleSTRUCTURAL VARIABILITY OF A-DNA IN CRYSTALS OF THE OCTAMER D(PCPCPCPGPCPGPGPG)
ComponentsDNA (5'-D(P*CP*CP*CP*GP*CP*GP*GP*G)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFernandez, L.G. / Subirana, J.A. / Verdaguer, N. / Pyshnyi, D. / Campos, L.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 1997
Title: Structural variability of A-DNA in crystals of the octamer d(pCpCpCpGpCpGpGpG)
Authors: Fernandez, L.G. / Subirana, J.A. / Verdaguer, N. / Pyshnyi, D. / Campos, L. / Malinina, L.
History
DepositionDec 19, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 3, 2017Group: Source and taxonomy / Structure summary
Revision 1.4Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,8572
Polymers4,8572
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.630, 40.590, 42.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 2428.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growpH: 6 / Details: pH 6.00
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2SPERMINE11
3MPD11
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mMNa-cacodylate1d
21.0 mMduplex1drop
32.0 mMspermine1drop
425.0 %MPD1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996 / Details: COLIMATOR 0.4
RadiationMonochromator: GRAFITO / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 3272 / % possible obs: 99.1 % / Redundancy: 5.765 % / Rmerge(I) obs: 0.032
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % possible obs: 99.1 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
MARXDSdata reduction
MARSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→8 Å / Cross valid method: R-FREE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.253 319 8.92 %RANDOM
Rwork0.19 ---
obs0.196 3262 89.98 %-
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-4 Å
Luzzati sigma a0.3 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 330 0 37 367
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na1.22
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.22
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.277 36 8.47 %
Rwork0.297 274 -
obs--72.94 %
Xplor fileSerial no: 1 / Param file: PARAM_NDBX.DNA / Topol file: TOP_NDBX.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 8.92 % / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_dihedral_angle_deg / Dev ideal: 8.23
LS refinement shell
*PLUS
Rfactor obs: 0.297

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