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Yorodumi- PDB-4gat: SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF ARE... -
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-Basic information
Entry | Database: PDB / ID: 4gat | ||||||
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Title | SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, REGULARIZED MEAN STRUCTURE | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / DNA BINDING PROTEIN / TRANSCRIPTION FACTOR / ZINC BINDING DOMAIN / COMPLEX (TRANSCRIPTION REGULATION-DNA) / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information regulation of amide catabolic process / regulation of arginine metabolic process / regulation of nitrogen utilization / nitrate assimilation / regulation of gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II ...regulation of amide catabolic process / regulation of arginine metabolic process / regulation of nitrogen utilization / nitrate assimilation / regulation of gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Emericella nidulans (mold) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Clore, G.M. / Starich, M. / Wikstrom, M. / Gronenborn, A.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors. Authors: Starich, M.R. / Wikstrom, M. / Arst Jr., H.N. / Clore, G.M. / Gronenborn, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 4gat.cif.gz | 58 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gat.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 4gat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gat_validation.pdf.gz | 300.8 KB | Display | wwPDB validaton report |
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Full document | 4gat_full_validation.pdf.gz | 300.5 KB | Display | |
Data in XML | 4gat_validation.xml.gz | 3.7 KB | Display | |
Data in CIF | 4gat_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/4gat ftp://data.pdbj.org/pub/pdb/validation_reports/ga/4gat | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 4009.637 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3933.558 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 7367.480 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Emericella nidulans (mold) / Gene: POTENTIAL / Organ: TAIL / Production host: Escherichia coli (E. coli) / References: UniProt: P17429 |
#4: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: DATA WERE RECORDED ON A 1:1 COMPLEX |
-Sample preparation
Sample conditions | pH: 6.1 / Temperature: 298 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
Software |
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NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 AND PROTEIN ENGINEERING 2, 27 - 38 USING THE PROGRAM X-PLOR MODIFIED ...Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 AND PROTEIN ENGINEERING 2, 27 - 38 USING THE PROGRAM X-PLOR MODIFIED TO INCORPORATE COUPLING CONSTANT RESTRAINTS (GARRETT ET AL. (1994) J. MAGN RESON. SERIES B 104, 99 - 103), CARBON CHEMICAL SHIFT RESTRAINTS (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92 - 96) RESTRAINTS, DIPOLAR COUPLING RESTRAINTS (TJANDRA ET AL. (1997) NATURE STRUCT BIOL 4, 732-738) AND A CONFORMATIONAL DATABASE POTENTIAL FOR PROTEINS AND NUCLEIC ACIDS (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, 1067 - 1080 AND (1997) J. MAGN. RESON. 125, 171-177) THE 3D STRUCTURE OF THE COMPLEX OF THE WILD TYPE AREA DBD-DNA COMPLEX WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON THE FOLLOWING 1098 EXPERIMENTAL RESTRAINTS (A) PROTEIN: 119 SEQUENTIAL (|I-J|=1), 49 SHORT RANGE (1 < |I-J| >=5), 68 LONG RANGE (|I-J|>5), AND 64 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; NULL 124 TORSION ANGLE RESTRAINTS (61 PHI, 8 PSI, 39 CHI1, 15 CHI2, AND 1 CHI3), 41 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; NULL 77 (41 CALPHA AND 36 CBETA) 13C CHEMICAL SHIFT RESTRAINTS; NULL 48 RESIDUAL N-H DIPOLAR COUPLING RESTRAINTS; 20 DISTANCE RESTRAINTS FOR 10 BACKBONE HYDROGEN BONDS. (B) DNA: 75 INTRARESIDUE, 115 SEQUENTIAL INTRASTRAND AND 20 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 66 DISTANCES FOR WATSON-CRICK BASE PAIR HYDROGEN BONDS; 170 TORSION ANGLE RESTRAINTS FOR THE DNA BACKBONE COVERING VALUES CHARACTERISTIC OF BOTH A AND B DNA. (C) 48 INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS (D) 2 INTERMOLECULAR DISTANCE RESTRAINTS TO PHOSPHATES (E) 8 'REPULSIVE' RESTRAINTS (F) 4 DISTANCE RESTRAINTS FOR 2 INTERMOLECULAR H-BONDS BETWEEN ARG 24 AND BASE OF GUA5. THE STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED MEAN STRUCTURE AND THE LAST NUMERIC COLUMN REPRESENTS THE RMS OF THE 35 INDIVIDUAL SIMULATED ANNEALING STRUCTURES FOUND IN PDB ENTRY 5GAT ABOUT THE MEAN COORDINATE POSITIONS. THE LAST NUMERIC COLUMN IN THE INDIVIDUAL SA STRUCTURES HAS NO MEANING. THE FOLLOWING TWO SETS OF COORDINATES DEFINE THE PRINCIPAL AXIS OF THE MAGNETIC SUSCEPTIBILITY TENSOR: POINT 1 115.014-147.742 -73.887 POINT 2 115.768-146.457 -73.538 | ||||||||||||
NMR ensemble | Conformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 35 / Conformers submitted total number: 1 |