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- PDB-1nzg: Crystal structure of A-DNA decamer GCGTA(3ME)ACGC, with a modifie... -

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Basic information

Entry
Database: PDB / ID: 1nzg
TitleCrystal structure of A-DNA decamer GCGTA(3ME)ACGC, with a modified 5-methyluridine
Components5'-D(*GP*CP*GP*TP*AP*(3ME)P*AP*CP*GP*C)-3'
KeywordsDNA / A-DNA / 2'-modified oligonucleotides
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPrhavc, M. / Prakash, T.P. / Minasov, G. / Egli, M. / Manoharan, M.
CitationJournal: Org.Lett. / Year: 2003
Title: 2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] modified oligonucleotides: symbiosis of charge interaction factors and stereoelectronic effects
Authors: Prhavc, M. / Prakash, T.P. / Minasov, G. / Cook, P.D. / Egli, M. / Manoharan, M.
History
DepositionFeb 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 2, 2011Group: Non-polymer description
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*CP*GP*TP*AP*(3ME)P*AP*CP*GP*C)-3'
B: 5'-D(*GP*CP*GP*TP*AP*(3ME)P*AP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,3522
Polymers6,3522
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.260, 44.110, 45.530
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 5'-D(*GP*CP*GP*TP*AP*(3ME)P*AP*CP*GP*C)-3'


Mass: 3176.178 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 1.71 Å3/Da / Density % sol: 27.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MPD, Sodium Cacodylate, Spermine, Sodium Chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Sodium Cacodylate11
3Spermine11
4Sodium Chloride11
5MPD12
6Sodium Chloride12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12000 nmoligonucleotide1drop
240 mMsodium cacodylate1droppH6.0
380 mM1dropNaCl
412 mMspermine tetrahydrochloride1drop
510 %(v/v)1drop
635 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 8, 1999 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 7031 / Num. obs: 7031 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 22.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 6.5 / Num. unique all: 575 / % possible all: 82.9
Reflection
*PLUS
Lowest resolution: 15 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: PARKINSON ET AL.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 687 -Random
Rwork0.192 ---
all-7114 --
obs-6676 93.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.756 Å20 Å20 Å2
2---10.058 Å20 Å2
3---7.302 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 422 0 101 523
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 1.6→1.64 Å
RfactorNum. reflection% reflection
Rfree0.353 35 -
Rwork0.312 --
obs--80.1 %
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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