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- PDB-399d: STRUCTURE OF D(CGCCCGCGGGCG) -

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Basic information

Entry
Database: PDB / ID: 399d
TitleSTRUCTURE OF D(CGCCCGCGGGCG)
ComponentsDNA (5'-D(*CP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*G)-3')
KeywordsDNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsMalinina, L. / Fernandez, L.G. / Subirana, J.A.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Structure of the d(CGCCCGCGGGCG) dodecamer: a kinked A-DNA molecule showing some B-DNA features.
Authors: Malinina, L. / Fernandez, L.G. / Huynh-Dinh, T. / Subirana, J.A.
History
DepositionMay 11, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Jan 18, 1999Provider: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,3312
Polymers7,3312
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.290, 42.602, 45.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 3665.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.99 Å3/Da / Density % sol: 38.09 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.6 / Details: pH 5.60, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PROTEIN (PHI0)11
3NA CITRATE11
4NACLSodium chloride11
5AMMONIUM ACETATE11
6PEG 400011
7WATER12
8PEG 400012
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.7 mMduplex1drop
20.5 mMprotein1drop
30.2 Msodium chloride1drop
40.15 mMammonium acetate1drop
50.05 Msodium citrate1drop
616 %(v/v)PEG40001drop
70.7 Mammonium acetate1reservoir
825 %(v/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: COLLIMATORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→22 Å / Num. obs: 4559 / % possible obs: 87.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 6.6 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 11
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.18 / % possible all: 79.7
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 22 Å / Num. obs: 4195 / % possible obs: 87.5 %
Reflection shell
*PLUS
% possible obs: 79.7 %

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→8 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: R-FREE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.203 407 8 %RANDOM
Rwork0.165 ---
obs0.165 3957 87.5 %-
Displacement parametersBiso mean: 12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 63 549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
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_deg1.624
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d17.103
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.913
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→1.97 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.25 28 6.28 %
Rwork0.25 265 -
obs--60.7 %
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
Rfactor obs: 0.211 / Rfactor Rfree: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg17.103
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.913
LS refinement shell
*PLUS
Rfactor obs: 0.25

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