- PDB-1kls: NMR Structure of the ZFY-6T[Y10L] Zinc Finger -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1kls
Title
NMR Structure of the ZFY-6T[Y10L] Zinc Finger
Components
ZINC FINGER Y-CHROMOSOMAL PROTEIN
Keywords
TRANSCRIPTION / Zinc Finger
Function / homology
Function and homology information
DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus Similarity search - Function
SOLUTION NMR / Distance geometry, Simulated annealing, , restrained molecular dynamics. The stereospecific assignments of the L10 methyl groups were determined by relaxation-matrix NOE backcalculation.
Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999
sequence The mutation Y10L was created for structural studies. In addition, the P2T mutation and C- ...sequence The mutation Y10L was created for structural studies. In addition, the P2T mutation and C-terminal K, originally introduced in ZFY-6T (PDB entry 5ZNF) improve sample behavior without affecting structure.
Mass: 3565.065 Da / Num. of mol.: 1 / Mutation: P2T, Y10L / Source method: obtained synthetically Details: This peptide was synthesized by solid-phase synthesis. The sequence of the peptide is naturally found in Homo sapiens (human). References: UniProt: P08048
Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D NOESY
1
2
2
2D NOESY
1
3
1
DQF-COSY
1
4
2
DQF-COSY
2
5
3
3D-TOCSY-NOESY
2
6
3
2D-ROESY
2
7
4
2D-ROESY
NMR details
Text: This structure was determined using 2D and 3D homonuclear techniques.Stereospecific assignments for the L18 methyl groups could not be unambiguously determined. However, the resonances were ...Text: This structure was determined using 2D and 3D homonuclear techniques.Stereospecific assignments for the L18 methyl groups could not be unambiguously determined. However, the resonances were clearly resolved. As a result,the structures were calculated as two families, depending on the assignments used. Structures 1-15 belong to one family, and use the assignments indicated in the accompanying restraint file. Structures 16-30 use the opposite assignments for the L18 methyls.
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
2mM ZFY-6T[Y10L]
90% H2O/10% D2O
2
2mM ZFY-6T[Y10L]
99.98% D2O.
3
5mM ZFY-6T[Y10L]
90% H2O/10% D2O
4
5mM ZFY-6T[Y10L]
99.98% D2O.
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
50mM d11-Tris-HCl, 2.2mM ZnCl2
6.0
ambient
298K
2
50mM d11-Tris-HCl, 5.5mM ZnCl2
6.0
ambient
298K
Crystal grow
*PLUS
Method: other / Details: NMR
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Varian VXRS
Varian
VXRS
500
1
Varian UNITYPLUS
Varian
UNITYPLUS
500
2
Varian INOVA
Varian
INOVA
500
3
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Processing
NMR software
Name
Version
Developer
Classification
VNMR
4.3, 5.3
Varian, Inc.
collection
VNMR
4.3, 5.3
Varian, Inc.
processing
NHFIT
Redfield, C.
dataanalysis
DGII
standalone
Havel, T.F.
structuresolution
X-PLOR
3.1
Brunger, A.T.
refinement
Refinement
Method: Distance geometry, Simulated annealing, , restrained molecular dynamics. The stereospecific assignments of the L10 methyl groups were determined by relaxation-matrix NOE backcalculation. Software ordinal: 1 Details: Structures are based on 265 interresidue NOE-derived distance constraints, 27 dihedral angle restraints, and 10 hydrogen bond restraints.
NMR representative
Selection criteria: fewest violations
NMR ensemble
Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 50 / Conformers submitted total number: 30
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