- PDB-1zr9: Solution Structure of a Human C2H2-type Zinc Finger Protein -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1zr9
Title
Solution Structure of a Human C2H2-type Zinc Finger Protein
Components
Zinc finger protein 593
Keywords
TRANSCRIPTION / zinc finger / DNA binding / Structural Genomics / PSI / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information
negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / preribosome binding / ribosome biogenesis / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / cytoplasm Similarity search - Function
SOLUTION NMR / Automated methods were used for backbone chemical shift assignment, iterative NOE refinement. Final structures were obtained by molecular dynamics in explicit solvent.
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
3D 13C-separated NOESY
1
2
1
3D 15N-separated NOESY
1
3
1
3D 13C-separated NOESY (AROMATIC)
NMR details
Text: All triple-resonance and NOESY spectra were acquired using a cyrogenic probe
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Sample preparation
Details
Contents: 0.6 mM ZNF593 U-15N,13C, 10 mM Bis Tris, 100 mM NaCl, 2 mM DTT, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O
Sample conditions
Ionic strength: 100 mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz
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Processing
NMR software
Name
Version
Developer
Classification
XwinNMR
3.5
BrukerBiospin
collection
NMRPipe
2004
F. Delaglio
processing
SPSCAN
1.1.0
R.W. Glaser
dataanalysis
XEASY
1.3
C. Bartels
dataanalysis
GARANT
2.1
C. Bartels
dataanalysis
CYANA
1.0.6
T. Herrmann, P. Guentert, K. Wuethrich
structuresolution
XPLOR-NIH
2.0.6
G. MariusClore
refinement
Refinement
Method: Automated methods were used for backbone chemical shift assignment, iterative NOE refinement. Final structures were obtained by molecular dynamics in explicit solvent. Software ordinal: 1 Details: Residues 1-27 and 95-116 of the construct were disordered and were excluded from the model. After initial calculations without zinc, the zinc atom was constrained in a tetrahedral geometry ...Details: Residues 1-27 and 95-116 of the construct were disordered and were excluded from the model. After initial calculations without zinc, the zinc atom was constrained in a tetrahedral geometry using distance restraints to each coordinating CYS SG and HIS NE2 of 2.3 A and 2.0 A, respectively.
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20
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