- 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
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
DNA (5'-D(*CP*AP*GP*CP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3')
DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*GP*CP*TP*G)-3')
NITROGEN REGULATORY PROTEIN AREA
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
Nitrogen regulatory AreA, N-terminal / Nitrogen regulatory protein AreA N terminus / Nitrogen regulatory protein areA, GATA-like domain / Fungal protein of unknown function (DUF1752) / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type ...Nitrogen regulatory AreA, N-terminal / Nitrogen regulatory protein AreA N terminus / Nitrogen regulatory protein areA, GATA-like domain / Fungal protein of unknown function (DUF1752) / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
B: DNA (5'-D(*CP*AP*GP*CP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3') C: DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*GP*CP*TP*G)-3') A: NITROGEN REGULATORY PROTEIN AREA hetero molecules
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 details
Text: DATA WERE RECORDED ON A 1:1 COMPLEX
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Sample preparation
Sample conditions
pH: 6.1 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker AMX500
Bruker
AMX500
360
1
Bruker DMX500
Bruker
DMX500
600
2
Bruker AMX600
Bruker
AMX600
500
3
Bruker DMX600
Bruker
DMX600
750
4
Bruker DMX750
Bruker
DMX750
750
5
Bruker AND AM360
Bruker
ANDAM360
750
6
Bruker 600
Bruker
600
750
7
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Processing
Software
Name
Version
Classification
X-PLOR
3.1
modelbuilding
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
NMR software
Name
Version
Developer
Classification
X-PLOR
3.1
BRUNGER
refinement
X-PLOR MODIFIED
MODIFIED
structuresolution
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
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