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- PDB-3uxw: Crystal Structures of an A-T-hook/DNA complex -

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Basic information

Entry
Database: PDB / ID: 3uxw
TitleCrystal Structures of an A-T-hook/DNA complex
Components
  • A-T hook peptide
  • dodecamer DNA
KeywordsDNA/PEPTIDE / A-T hook-DNA complex / oligonucletide duplex HMGA-1a protein / DNA-PEPTIDE complex
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsFonfria-Subiros, E. / Acosta-Reyes, F.J. / Saperas, N. / Pous, J. / Subirana, J.A. / Campos, J.L.
CitationJournal: Plos One / Year: 2012
Title: Crystal structure of a complex of DNA with one AT-hook of HMGA1.
Authors: Fonfria-Subiros, E. / Acosta-Reyes, F. / Saperas, N. / Pous, J. / Subirana, J.A. / Campos, J.L.
History
DepositionDec 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dodecamer DNA
B: dodecamer DNA
C: dodecamer DNA
D: dodecamer DNA
E: dodecamer DNA
F: dodecamer DNA
G: dodecamer DNA
H: dodecamer DNA
K: A-T hook peptide
L: A-T hook peptide
M: A-T hook peptide
N: A-T hook peptide


Theoretical massNumber of molelcules
Total (without water)33,79712
Polymers33,79712
Non-polymers00
Water1,06359
1
A: dodecamer DNA
B: dodecamer DNA
N: A-T hook peptide


Theoretical massNumber of molelcules
Total (without water)8,4493
Polymers8,4493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-3 kcal/mol
Surface area4660 Å2
MethodPISA
2
C: dodecamer DNA
D: dodecamer DNA
M: A-T hook peptide


Theoretical massNumber of molelcules
Total (without water)8,4493
Polymers8,4493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-2 kcal/mol
Surface area4860 Å2
MethodPISA
3
E: dodecamer DNA
F: dodecamer DNA
K: A-T hook peptide


Theoretical massNumber of molelcules
Total (without water)8,4493
Polymers8,4493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-5 kcal/mol
Surface area4940 Å2
MethodPISA
4
G: dodecamer DNA
H: dodecamer DNA
L: A-T hook peptide


Theoretical massNumber of molelcules
Total (without water)8,4493
Polymers8,4493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-5 kcal/mol
Surface area4740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.143, 66.855, 50.052
Angle α, β, γ (deg.)90.00, 111.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain
dodecamer DNA


Mass: 3661.416 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: Phosphoramidite method
#2: Protein/peptide
A-T hook peptide


Mass: 1126.425 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 6, 2011 / Details: Mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 19462 / % possible obs: 94.3 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2-2.03156.4
2.03-2.07170.1
2.07-2.11186.8
2.11-2.15193.7
2.15-2.2197.2
2.2-2.25197.7
2.25-2.31198.2
2.31-2.37198.5
2.37-2.44198.1
2.44-2.52198.7
2.52-2.61198.5
2.61-2.71198.6
2.71-2.84198.8
2.84-2.99199
2.99-3.17198.8
3.17-3.42198.6
3.42-3.76199.3
3.76-4.31199.4
4.31-5.42199.5
5.42-40198.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→37.76 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.441 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.385 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2771 740 5.3 %RANDOM
Rwork0.21949 ---
obs0.22266 13163 98.76 %-
all-19462 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.433 Å2
Baniso -1Baniso -2Baniso -3
1-3.33 Å20 Å20.9 Å2
2---3.85 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.27→37.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms294 1944 0 59 2297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122461
X-RAY DIFFRACTIONr_angle_refined_deg2.2211.4373710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.964530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg0.67109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.2461572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.698159
X-RAY DIFFRACTIONr_chiral_restr0.1030.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211205
LS refinement shellResolution: 2.27→2.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 47 -
Rwork0.321 947 -
obs--98.12 %

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