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- PDB-2plo: D-(GTATACC) low temperature (100K) -

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Basic information

Entry
Database: PDB / ID: 2plo
TitleD-(GTATACC) low temperature (100K)
Components5'-D(*DGP*DGP*DTP*DAP*DTP*DAP*DCP*DC)-3'
KeywordsDNA / HIGH PRESSURE / LOW TEMPERATURE / COMPRESSIBILITY / CRYSTALS
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsPrange, T. / Lecouvey, M. / Migianu-Griffoni, E.
Citation
Journal: To be Published
Title: Adaptation of macromolecular crystals to extreme conditions: high pressure versus low temperature
Authors: Prange, T. / Girard, E. / Kahn, R. / Lecouvey, M. / Migianu-Griffoni, E. / Mezouar, M. / Fourme, R.
#1: Journal: To be Published
Title: Adaptation of base paired double helix 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.
History
DepositionApr 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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)4,8763
Polymers4,8532
Non-polymers231
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-9.7 kcal/mol
Surface area3110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.783, 44.783, 41.393
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsA form of DNA - double stranded helix

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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: automated solid synthesis
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20 mg dissolved in 0.2 ml of 15 % MPD, 10-2 M sodium cacodylate buffer. Additives : 10-5M sodium azide, 10-2 M MgCl2 and 2.10-2 M spermine chloride, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3sodium azide11
4MgCl211
5spermine chloride11
6MPD12
7sodium cacodylate12
8sodium azide12
9MgCl212
10spermine chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.962 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2006 / Details: Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.962 Å / Relative weight: 1
ReflectionResolution: 1.4→10 Å / Num. obs: 9382 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.2
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 3.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SHELXL-97refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2PL8

2pl8


Resolution: 1.4→10 Å / Num. parameters: 1579 / Num. restraintsaints: 1606 / Isotropic thermal model: individual isotropic B factors / Cross valid method: NONE / σ(F): 2 / σ(I): 4
RfactorNum. reflection% reflection
Rwork0.17 --
all0.1796 9357 -
obs0.1773 8870 100 %
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 182 / Occupancy sum non hydrogen: 393
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 322 1 70 393
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.098
X-RAY DIFFRACTIONs_angle_d0.295
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0005
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.015
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.026
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.027
X-RAY DIFFRACTIONs_approx_iso_adps0

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