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- PDB-1xjy: The crystal structures of the DNA binding sites of the RUNX1 tran... -

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Basic information

Entry
Database: PDB / ID: 1xjy
TitleThe crystal structures of the DNA binding sites of the RUNX1 transcription factor
Components
  • 5'-D(*TP*CP*TP*GP*CP*GP*GP*TP*C)-3'
  • 5'-D(*TP*GP*AP*CP*CP*GP*CP*AP*G)-3'
KeywordsDNA / A-DNA / DOUBLE HELIX / OVERHANGING BASES / RUNX1
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKitayner, M. / Rozenberg, H. / Rabinovich, D. / Shakked, Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structures of the DNA-binding site of Runt-domain transcription regulators.
Authors: Kitayner, M. / Rozenberg, H. / Rabinovich, D. / Shakked, Z.
History
DepositionSep 26, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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(*TP*CP*TP*GP*CP*GP*GP*TP*C)-3'
B: 5'-D(*TP*GP*AP*CP*CP*GP*CP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)5,4642
Polymers5,4642
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.295, 42.295, 24.333
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 2722.784 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*GP*AP*CP*CP*GP*CP*AP*G)-3'


Mass: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.99 Å3/Da / Density % sol: 38.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: OSMIC CONFOCAL MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
21.54181
ReflectionResolution: 2→19 Å / Num. obs: 2975 / % possible obs: 100 % / Redundancy: 7.1 % / Rsym value: 0.042 / Net I/σ(I): 52.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 8.9 / Rsym value: 0.261 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
ULTIMAmodel building
SHELXL-97refinement
ULTIMAphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FIBER A-DNA

Resolution: 2→15 Å / Num. parameters: 1696 / Num. restraintsaints: 5755 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: L.CLOWNEY ET AL.,J.AM.CHEM.SOC.118(1996)509-518, A.GELBIN ET AL.,J.AM.CHEM.SOC.118(1996)519-529, G.PARKINSON ET AL.,ACTA CRYST.D52(1996)57-64
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 146 5 %RANDOM
Rwork0.1407 ---
all0.1418 2931 --
obs0.1418 -97.2 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 420
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 330 0 90 420
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0.021
X-RAY DIFFRACTIONs_from_restr_planes0.0005
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.006
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.112
X-RAY DIFFRACTIONs_approx_iso_adps0

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