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Yorodumi- PDB-1xrz: NMR Structure of a Zinc Finger with Cyclohexanylalanine Substitut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xrz | ||||||
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Title | NMR Structure of a Zinc Finger with Cyclohexanylalanine Substituted for the Central Aromatic Residue | ||||||
Components | Zinc finger Y-chromosomal protein | ||||||
Keywords | TRANSCRIPTION / cyclohexanylalanine / zinc finger | ||||||
Function / homology | Function and homology information DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 ...DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 / nucleus / metal ion binding Similarity search - Function | ||||||
Method | SOLUTION NMR / Distance geometry, simulated annealing, restrained molecular dynamics | ||||||
Authors | Lachenmann, M.J. / Ladbury, J.E. / Qian, X. / Huang, K. / Singh, R. / Weiss, M.A. | ||||||
Citation | Journal: Protein Sci. / Year: 2004 Title: Solvation and the hidden thermodynamics of a zinc finger probed by nonstandard repair of a protein crevice Authors: Lachenmann, M.J. / Ladbury, J.E. / Qian, X. / Huang, K. / Singh, R. / Weiss, M.A. | ||||||
History |
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Remark 999 | SEQUENCE LYS A 30 WAS ENGINEERED TO IMPROVE SAMPLE SOLUBILITY WHILE NOT AFFECTING THE STRUCTURE |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xrz.cif.gz | 334.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xrz.ent.gz | 290.5 KB | Display | PDB format |
PDBx/mmJSON format | 1xrz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xrz_validation.pdf.gz | 355.8 KB | Display | wwPDB validaton report |
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Full document | 1xrz_full_validation.pdf.gz | 538.8 KB | Display | |
Data in XML | 1xrz_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 1xrz_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/1xrz ftp://data.pdbj.org/pub/pdb/validation_reports/xr/1xrz | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3605.129 Da / Num. of mol.: 1 Fragment: sequence database residues 570-598: contains C2H2-type 6 Zinc Finger (residues 572-595) Mutation: P2T, Y10(HAC) / Source method: obtained synthetically Details: The protein was chemically synthesized using solid-phase peptide synthesis. The ZFY protein is naturally found in Homo Sapiens (Human). References: UniProt: P08048 |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques. Hydrogen assignments for the cyclohexanyl ring were made by extension from the normal methods. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 50mM D11-Tris-HCl, 2.2mM ZnCl2 / pH: 6.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: Distance geometry, simulated annealing, restrained molecular dynamics Software ordinal: 1 | ||||||||||||||||||||||||
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: 34 |