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- PDB-1ilc: DNA Bending by an Adenine-Thymine Tract and Its Role in Gene Regu... -

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Basic information

Entry
Database: PDB / ID: 1ilc
TitleDNA Bending by an Adenine-Thymine Tract and Its Role in Gene Regulation.
Components5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
KeywordsDNA / B-DNA DOUBLE HELIX / DODECAMER DUPLEX / HPV E2 DNA TARGET
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHizver, J. / Rozenberg, H. / Frolow, F. / Rabinovich, D. / Shakked, Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: DNA bending by an adenine--thymine tract and its role in gene regulation.
Authors: Hizver, J. / Rozenberg, H. / Frolow, F. / Rabinovich, D. / Shakked, Z.
History
DepositionMay 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
B: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
C: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
D: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
E: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
F: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)21,9746
Polymers21,9746
Non-polymers00
Water2,054114
1
A: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
B: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
D: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
F: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.821, 40.160, 39.460
Angle α, β, γ (deg.)74.42, 76.44, 59.90
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 3662.404 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Human papillomavirus E2 DNA target
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.29 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, magnesium chloride, spermine.4HCl, Na cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Mg2Cl11
3spermine.4HCl11
4Na cacodylate11
5MPD12
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12 mg/mlDNA1drop
276 mM1dropMgCl2
31 mMspermine-4HCl1drop
420 mMsodium cacodylate1droppH7.0
515 %(w/v)1drop
637 %(w/v)MPD1reservoir
720 mMsodium cacodylate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 10, 1997 / Details: Yale-type mirrors
RadiationMonochromator: Ni filter + Yale-type mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→19 Å / Num. all: 9810 / Num. obs: 9810 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 25.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2 / Num. unique all: 491 / Rsym value: 0.654 / % possible all: 95
Reflection
*PLUS
Num. measured all: 36389 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 95 % / Rmerge(I) obs: 0.564

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Processing

Software
NameVersionClassification
MFTmodel building
ULTIMAmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MFTphasing
ULTIMAphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fiber model of B-DNA

Resolution: 2.2→19 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Parkinson et al.
Details: REFINEMENT STARTED WITH X-PLOR 3.1 USING B-DNA FIBER MODEL ALL DATA INCLUDED. REFINEMENT CONTINUED IN SHELXL-97 WITH THE OPTION HOPE FOR ANISOTROPIC SCALING TO CORRECT SIGNIFICANT ANISOTROPY ...Details: REFINEMENT STARTED WITH X-PLOR 3.1 USING B-DNA FIBER MODEL ALL DATA INCLUDED. REFINEMENT CONTINUED IN SHELXL-97 WITH THE OPTION HOPE FOR ANISOTROPIC SCALING TO CORRECT SIGNIFICANT ANISOTROPY IN THE DATA. THE CORRECTED OBSERVED STRUCTURE FACTORS WITH F<0 WERE EXCLUDED FROM REFINEMENT. REFINEMENT FURTHER CONTINUED WITH X-PLOR 3.1.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 456 -random
Rwork0.222 ---
obs0.224 8475 86.4 %-
all-9810 --
Displacement parametersBiso mean: 30.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1458 0 114 1572
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d17.7
LS refinement shellResolution: 2.2→2.3 Å /
RfactorNum. reflection
Rfree0.37 37
Rwork0.33 -
Xplor fileSerial no: 1 / Param file: PARAM_NDBX.DNA / Topol file: TOP_NDBX.DNA
Refinement
*PLUS
Num. reflection obs: 8474 / % reflection Rfree: 5 % / Rfactor obs: 0.224 / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg17.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.37 / Rfactor Rwork: 0.33 / Rfactor obs: 0.33

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