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- PDB-344d: DETERMINATION BY MAD-DM OF THE STRUCTURE OF THE DNA DUPLEX D(ACGT... -

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Basic information

Entry
Database: PDB / ID: 344d
TitleDETERMINATION BY MAD-DM OF THE STRUCTURE OF THE DNA DUPLEX D(ACGTACG(5-BRU))2 AT 1.46A AND 100K
ComponentsDNA (5'-D(*AP*CP*GP*TP*AP*CP*GP*(BRU))-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.46 Å
AuthorsTodd, A.R. / Adams, A. / Powell, H.R. / Cardin, C.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Determination by MAD-DM of the structure of the DNA duplex d[ACGTACG(5-BrU)]2 at 1.46 A and 100 K.
Authors: Todd, A.K. / Adams, A. / Powell, H.R. / Wilcock, D.J. / Thorpe, J.H. / Lausi, A. / Zanini, F. / Wakelin, L.P. / Cardin, C.J.
History
DepositionAug 4, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 26, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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*GP*TP*AP*CP*GP*(BRU))-3')


Theoretical massNumber of molelcules
Total (without water)2,4911
Polymers2,4911
Non-polymers00
Water1,58588
1
A: DNA (5'-D(*AP*CP*GP*TP*AP*CP*GP*(BRU))-3')

A: DNA (5'-D(*AP*CP*GP*TP*AP*CP*GP*(BRU))-3')


Theoretical massNumber of molelcules
Total (without water)4,9832
Polymers4,9832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)43.597, 43.597, 26.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-54-

HOH

21A-74-

HOH

31A-92-

HOH

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Components

#1: DNA chain DNA (5'-D(*AP*CP*GP*TP*AP*CP*GP*(BRU))-3')


Mass: 2491.487 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 285 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 mMDNA1drop
250 mMcacodylate1drop
32.0 mMmagnesium acetate1drop
43.0 mMsperine-4HCl1drop
55 %MPD1drop
630 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 14, 1996 / Details: MIRROR
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.4→15 Å / Num. obs: 8062 / % possible obs: 98.3 % / Redundancy: 4.35 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 0.137
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.137 / % possible all: 60.1
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 15 Å / % possible obs: 98.3 % / Redundancy: 4.35 %
Reflection shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.45 Å / % possible obs: 60.1 % / Redundancy: 1.1 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
DM(CCP4 VERSIONS)model building
SHELXL-96refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MAD
Starting model: NDB ENTRY ADH070 (PDB ENTRY 243D)

243d


Highest resolution: 1.46 Å / Num. parameters: 2232 / Num. restraintsaints: 2730 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT
RfactorNum. reflection% reflection
obs0.1115 4555 96.5 %
all-4555 -
Solvent computationSolvent model: MOEWS & KRETSINGER,J.MOL.BIOL.91(1973)201
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 245
Refinement stepCycle: LAST / Highest resolution: 1.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 88 249
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d0.006
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-96 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 4312 / σ(F): 0 / Rfactor all: 0.1115 / Rfactor obs: 0.109 / Rfactor Rfree: 0.2003
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.059
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.3

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