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- PDB-2plb: D(GTATACC) under hydrostatic pressure of 1.39 GPa -

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Basic information

Entry
Database: PDB / ID: 2plb
TitleD(GTATACC) under hydrostatic pressure of 1.39 GPa
Components5'-D(*DGP*DGP*DTP*DAP*DTP*DAP*DCP*DC)-3'
KeywordsDNA / HIGH-PRESSURE
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsPrange, T. / Girard, E. / Kahn, R. / Fourme, R.
Citation
Journal: Nucleic Acids Res. / Year: 2007
Title: Adaptation of the base-paired double-helix molecular architecture to extreme pressure.
Authors: Girard, E. / Prange, T. / Dhaussy, A.C. / Migianu-Griffoni, E. / Lecouvey, M. / Chervin, J.C. / Mezouar, M. / Kahn, R. / Fourme, R.
#1: Journal: Nature / Year: 1989
Title: Coexistence of A-and B-Form DNA in a Single Crystal Lattice
Authors: Doucet, J. / Benoit, J.-P. / Cruse, W.B.T. / Prange, T. / Kennard, O.
#2: Journal: J.Synchrotron Radia. / Year: 2001
Title: High-pressure protein crystallography (HPPX): Instrumentation, methodology and results on lysozyme crystals
Authors: Fourme, R. / Kahn, R. / Mezouar, M. / Girard, E. / Horentrup, C. / Prange, T. / Ascone, I.
#3: Journal: BIOCHEM.BIOPHYS.ACTA PROTEINS & PROTEOMICS / Year: 2006
Title: High pressure macromolecular crystallography: The 140 MPa crystal structure at 2.3 A resolution of urate oxidase, A 135 KD tetrameric assembly
Authors: Colloc'h, N. / Girard, E. / Dhaussy, A.C. / Kahn, R. / Ascone, I. / Mezouar, M. / Fourme, R.
History
DepositionApr 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*DGP*DGP*DTP*DAP*DTP*DAP*DCP*DC)-3'
B: 5'-D(*DGP*DGP*DTP*DAP*DTP*DAP*DCP*DC)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0563
Polymers4,8532
Non-polymers2021
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.830, 42.830, 40.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: DNA chain 5'-D(*DGP*DGP*DTP*DAP*DTP*DAP*DCP*DC)-3'


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA octamer
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.11 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20 mg of DNA dissolved in 0.2 ml of 15% MPD solution cacodylate buffer 10-2 M. Additives: 10-5 M sodium azide, 10-2 M MgCl2, 2.10-2 M spermine chloride. Reservoir: same solution but 50 % ...Details: 20 mg of DNA dissolved in 0.2 ml of 15% MPD solution cacodylate buffer 10-2 M. Additives: 10-5 M sodium azide, 10-2 M MgCl2, 2.10-2 M spermine chloride. Reservoir: same solution but 50 % MPD, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
115% MPD11
2cacodylate buffer11
3sodium azide11
4MgCl211
5spermine chloride11
650% MPD12
7cacodylate buffer12
8sodium azide12
9MgCl212
10spermine chloride12

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID27 / Wavelength: 0.3738 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 10, 2006 / Details: 2 crystals, parallel beam, no focusing
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.3738 Å / Relative weight: 1
ReflectionResolution: 1.6→10 Å / Num. all: 5582 / Num. obs: 5518 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.1 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.4
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.2 / Num. unique all: 490 / % possible all: 99

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
AUTOMARdata collection
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2PL8

2pl8


Resolution: 1.6→10 Å / Num. parameters: 1747 / Num. restraintsaints: 1776 / Isotropic thermal model: individual restrained B factors / Cross valid method: FREE R / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH AND HUBER
Details: One sugar and one phosphate group are disordered (two positions). The spermine molecule is also disordered
RfactorNum. reflection% reflectionSelection details
Rfree0.222 440 -RANDOM
Rwork0.1806 ---
all0.219 5582 --
obs0.1866 5518 99.9 %-
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 178 / Occupancy sum non hydrogen: 412
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 322 14 76 412
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0011
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.008
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.063
X-RAY DIFFRACTIONs_approx_iso_adps0

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