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- PDB-1enn: SOLVENT ORGANIZATION IN AN OLIGONUCLEOTIDE CRYSTAL: THE STRUCTURE... -

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Basic information

Entry
Database: PDB / ID: 1enn
TitleSOLVENT ORGANIZATION IN AN OLIGONUCLEOTIDE CRYSTAL: THE STRUCTURE OF D(GCGAATTCG)2 AT ATOMIC RESOLUTION
ComponentsDNA (5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*G)-3')
KeywordsDNA / B-DNA / ATOMIC RESOLUTION / IONS / HYDRATION / BASE TRIPLET
Function / homologyOXYGEN ATOM / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.89 Å
AuthorsSoler-Lopez, M. / Malinina, L. / Subirana, J.A.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Solvent organization in an oligonucleotide crystal. The structure of d(GCGAATTCG)2 at atomic resolution.
Authors: Soler-Lopez, M. / Malinina, L. / Subirana, J.A.
History
DepositionMar 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
SupersessionJul 20, 2001ID: 475D
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,76513
Polymers5,5122
Non-polymers25411
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)21.938, 36.540, 52.728
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(*GP*CP*GP*AP*AP*TP*TP*CP*G)-3')


Mass: 2755.823 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 1.84 Å3/Da / Density % sol: 33.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.1
Details: ACRIDINE-(ARG)4 ADDUCT, CACODYLATE, MGCL2, MPD, pH 7.1, vapor diffusion at 293K, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1ACRIDINE-(ARG)4 ADDUCT11
2CACODYLATE11
3MGCL211
4MPD11
5MGCL212
6MPD12
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaSol-ID
10.5 mMDNA duplex1
21 mMacridine-(Arg4) drug-peptide aduct1
320 mMsodium cacodylate1
4100 mM1MgCl2
535 %MPD11
61

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 0.89→30 Å / Num. all: 320317 / Num. obs: 32684 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.059
Reflection shellResolution: 0.89→0.9 Å / Redundancy: 1.43 % / Rmerge(I) obs: 0.3 / % possible all: 59
Reflection shell
*PLUS
% possible obs: 59 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
SHELXL-97refinement
X-PLORphasing
RefinementResolution: 0.89→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Details: 'OXYGEN ATOMS' 179, 180, 181 REPRESENT ADDITIONAL PEAKS OF ELECTRON DENSITY FOUND AT DISTANCES 0.9-1.4 A FROM EITHER ATOM OF THE PHOSPHATE GROUPS 9, 12, 14. MOST LIKELY, THESE THREE ...Details: 'OXYGEN ATOMS' 179, 180, 181 REPRESENT ADDITIONAL PEAKS OF ELECTRON DENSITY FOUND AT DISTANCES 0.9-1.4 A FROM EITHER ATOM OF THE PHOSPHATE GROUPS 9, 12, 14. MOST LIKELY, THESE THREE 'OXYGENS' ARE A SIGN OF DISORDER OF THESE PHOSPHATES AND WERE REFINED AS OXYGEN ATOMS.
RfactorNum. reflection% reflectionSelection details
Rfree0.161 3201 10 %RANDOM
Rwork0.135 ---
all0.14 32479 --
obs0.135 29278 97.6 %-
Refinement stepCycle: LAST / Resolution: 0.89→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 391 8 169 568
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d2.6
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.6

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