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- PDB-1bdn: CRYSTAL LATTICE PACKING IS IMPORTANT IN DETERMINING THE BEND OF A... -

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Basic information

Entry
Database: PDB / ID: 1bdn
TitleCRYSTAL LATTICE PACKING IS IMPORTANT IN DETERMINING THE BEND OF A DNA DODECAMER CONTAINING AN ADENINE TRACT
Components
  • DNA (5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*TP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*AP*TP*TP*TP*TP*TP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsDiGabriele, A.D. / Sanderson, M.R. / Steitz, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1989
Title: Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract.
Authors: DiGabriele, A.D. / Sanderson, M.R. / Steitz, T.A.
History
DepositionJul 25, 1989Deposition site: BNL / Processing site: BNL
Revision 1.0Apr 15, 1991Provider: repository / Type: Initial release
Revision 1.1May 22, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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(*CP*GP*CP*AP*AP*AP*AP*AP*TP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*AP*TP*TP*TP*TP*TP*GP*CP*G)-3')
C: DNA (5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*TP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*AP*TP*TP*TP*TP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6986
Polymers14,6504
Non-polymers492
Water37821
1
A: DNA (5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*TP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*AP*TP*TP*TP*TP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3493
Polymers7,3252
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*TP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*AP*TP*TP*TP*TP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3493
Polymers7,3252
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.540, 40.320, 65.860
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(*CP*GP*CP*AP*AP*AP*AP*AP*TP*GP*CP*G)-3')


Mass: 3680.432 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*CP*AP*TP*TP*TP*TP*TP*GP*CP*G)-3')


Mass: 3644.376 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 283.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4NA CACODYLATE11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlDNA solution1reservoir
244 mM1reservoirMgCl2
310 mMsodium cacodylate1reservoir
440 %(v/v)MPD1reservoir
51
61

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Data collection

DiffractionMean temperature: 285 K
DetectorType: UCSD MARK II / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 2267 / Observed criterion σ(I): 0.5

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Processing

SoftwareName: CORELS / Classification: refinement
RefinementResolution: 2.6→8 Å / σ(I): 0.5 /
RfactorNum. reflection
obs0.201 1975
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 972 2 21 995

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