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- PDB-1dnz: A-DNA DECAMER ACCGGCCGGT WITH MAGNESIUM BINDING SITES -

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Basic information

Entry
Database: PDB / ID: 1dnz
TitleA-DNA DECAMER ACCGGCCGGT WITH MAGNESIUM BINDING SITES
ComponentsDNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3')
KeywordsDNA / DNA CONFORMATION / METAL IONS
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRobinson, H. / Gao, Y.-G. / Sanishvili, R. / Joachimiak, A. / Wang, A.H.-J.
CitationJournal: Nucleic Acids Res. / Year: 2000
Title: Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.
Authors: Robinson, H. / Gao, Y.G. / Sanishvili, R. / Joachimiak, A. / Wang, A.H.
History
DepositionDec 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: 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 / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,0953
Polymers3,0461
Non-polymers492
Water64936
1
A: DNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3')
hetero molecules

A: DNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1896
Polymers6,0922
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)38.502, 38.502, 77.631
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Cell settinghexagonal
Space group name H-MP6122

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Components

#1: DNA chain DNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3')


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.44 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPD, CACODYLATE, MGCL2, SPERMINE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1CACODYLATE11
2SPERMINE11
3MGCL211
4MPD11
5MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDDetailsSol-IDChemical formula
15 mMDNA duplex10.0025ml
2100 mMsodium cacodylate10.0010ml
320 %MPD10.005ml
415 mMspermine10.0025ml
5100 mM10.0025ml1MgCl2

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 4901 / Num. obs: 4901 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.2 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 47.8
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 9.2 / % possible all: 96.8
Reflection
*PLUS

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
d*TREKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / Num. parameters: 963 / Num. restraintsaints: 907 / Cross valid method: A POSTERIORI / σ(F): 0 / σ(I): 0 / Stereochemistry target values: G.PARKINSON ET AL.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 245 5 %RANDOM
Rwork0.227 ---
all0.229 4874 --
obs0.227 4874 99.6 %-
Solvent computationSolvent model: SHELXL SWAT OPTION
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 235.5
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 14 24 240
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.071
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.003
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.06
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_plane_restr0.071

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