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- PDB-2h9s: Crystal Structure of Homo-DNA and Nature's Choice of Pentose over... -

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Basic information

Entry
Database: PDB / ID: 2h9s
TitleCrystal Structure of Homo-DNA and Nature's Choice of Pentose over Hexose in the Genetic System
Components5'-D(*(XCT)P*(XGU)P*(XAD)P*(XAD)P*(XTH)P*(XTH)P*(XCT)P*(XGU))-3'
KeywordsDNA / Homo-DNA / Homo-DNA crystal structure / 2' / 3'-Di-deoxy-beta- D-glucopyranose / Hexose nucleic acid / Glucopyranosyl nucleic acid / Dideoxyglucopyranose Octamer
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsEgli, M. / Pallan, P.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system.
Authors: Egli, M. / Pallan, P.S. / Pattanayek, R. / Wilds, C.J. / Lubini, P. / Minasov, G. / Dobler, M. / Leumann, C.J. / Eschenmoser, A.
History
DepositionJun 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues ...pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / 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(*(XCT)P*(XGU)P*(XAD)P*(XAD)P*(XTH)P*(XTH)P*(XCT)P*(XGU))-3'
B: 5'-D(*(XCT)P*(XGU)P*(XAD)P*(XAD)P*(XTH)P*(XTH)P*(XCT)P*(XGU))-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1023
Polymers5,0782
Non-polymers241
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.940, 38.940, 133.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-216-

HOH

21B-53-

HOH

31B-58-

HOH

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Components

#1: DNA chain 5'-D(*(XCT)P*(XGU)P*(XAD)P*(XAD)P*(XTH)P*(XTH)P*(XCT)P*(XGU))-3'


Mass: 2538.831 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically Synthesized
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.5 mM homo-DNA, 8 mM Sodium Cacodylate (pH 7.0), 6 mM Magnesium Chloride, 12% MPD (2-methyl-2,4-pentanediol), VAPOR DIFFUSION, SITTING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium Cacodylate11
2Magnesium Chloride11
3MPD (2-methyl-2,4-pentanediol)11
4H2O11
5Sodium Cacodylate12
6Magnesium Chloride12
7H2O12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 6, 2000
RadiationMonochromator: Double crystal Si(111) cryogenically cooled monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 6688 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 9.9
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 9.9 / Num. unique all: 638 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
CNSrefinement
DENZOdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→20 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 658 -Random
Rwork0.24 ---
obs0.24 6652 99.5 %-
all-6688 --
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 364 6 67 437
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg1.17
X-RAY DIFFRACTIONr_bond_refined_d0.015

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