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- PDB-7gat: SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF A... -

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Basic information

Entry
Database: PDB / ID: 7gat
TitleSOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13 BP DNA CONTAINING A TGATA SITE, 34 STRUCTURES
Components
  • DNA (5'-D(*CP*AP*GP*TP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3')
  • DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*AP*CP*TP*G)-3')
  • NITROGEN REGULATORY PROTEIN AREA
KeywordsTRANSCRIPTION/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 / Nitrogen regulatory protein areA, GATA-like domain / 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 / Nitrogen regulatory protein areA, GATA-like domain / 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
DNA / DNA (> 10) / Nitrogen regulatory protein areA
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodSOLUTION NMR / simulated annealing
AuthorsClore, G.M. / Starich, M. / Wikstrom, M. / Gronenborn, A.M.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: The solution structure of the Leu22-->Val mutant AREA DNA binding domain complexed with a TGATAG core element defines a role for hydrophobic packing in the determination of specificity.
Authors: Starich, M.R. / Wikstrom, M. / Schumacher, S. / Arst Jr., H.N. / Gronenborn, A.M. / Clore, G.M.
History
DepositionNov 7, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.content_type / _pdbx_database_related.details / _pdbx_database_status.process_site / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*AP*GP*TP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3')
C: DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*AP*CP*TP*G)-3')
A: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3614
Polymers15,2963
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)34 / 34
Representative

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Components

#1: DNA chain DNA (5'-D(*CP*AP*GP*TP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3')


Mass: 4024.649 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*AP*CP*TP*G)-3')


Mass: 3917.559 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein NITROGEN REGULATORY PROTEIN AREA


Mass: 7353.453 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN / Mutation: L22V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Gene: POTENTIAL / Production host: Escherichia coli (E. coli) / References: UniProt: P17429
#4: Chemical ChemComp-ZN / ZINC ION


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

ExperimentMethod: SOLUTION NMR
NMR detailsText: DATA WERE RECORDED ON A 1:1 COMPLEX

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Sample preparation

Sample conditionspH: 6.1 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AM360BrukerAM3603601
Bruker AMX500BrukerAMX5005002
Bruker DMX500BrukerDMX5005003
Bruker AMX600BrukerAMX6006004
Bruker DMX600BrukerDMX6006005
Bruker DMX750BrukerDMX7507506

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR MODIFIEDMODIFIEDstructure solution
RefinementMethod: 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 LEU22VAL AREA DBD-DNA COMPLEX WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON THE FOLLOWING 1128 EXPERIMENTAL RESTRAINTS (A) PROTEIN: 131 SEQUENTIAL (|I-J|=1), 63 SHORT RANGE (1 < |I-J| >=5), 67 LONG RANGE (|I-J|>5), AND 38 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; NULL 120 TORSION ANGLE RESTRAINTS (53 PHI, 13 PSI, 39 CHI1, 14 CHI2, AND 1 CHI3), 39 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; NULL 75 (41 CALPHA AND 34 CBETA) 13C CHEMICAL SHIFT RESTRAINTS; NULL 49 RESIDUAL N-H DIPOLAR COUPLING RESTRAINTS; 20 DISTANCE RESTRAINTS FOR 10 BACKBONE HYDROGEN BONDS. (B) DNA: 75 INTRARESIDUE, 124 SEQUENTIAL INTRASTRAND AND 22 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 63 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) 58 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 FOLLOWING TWO SETS OF COORDINATES DEFINE THE PRINCIPAL AXIS OF THE MAGNETIC SUSCEPTIBILITY TENSOR: MODEL 1 POINT 1 107.655-208.946-106.193 POINT 2 108.451-207.744-105.681 MODEL 2 POINT 1 24.256-113.704-161.840 POINT 2 25.068-112.489-161.388 MODEL 3 POINT 1 110.722 -57.479 -91.565 POINT 2 111.513 -56.276 -91.046 MODEL 4 POINT 1 186.368 -55.854 -82.498 POINT 2 187.151 -54.644 -81.982 MODEL 5 POINT 1 155.528 -80.412 -69.758 POINT 2 156.317 -79.202 -69.251 MODEL 6 POINT 1 26.237-154.854-147.679 POINT 2 26.981-153.617-147.173 MODEL 7 POINT 1 40.402 -54.390 -4.361 POINT 2 41.211 -53.217 -3.802 MODEL 8 POINT 1 126.627-223.740 -96.339 POINT 2 127.453-222.567 -95.808 MODEL 9 POINT 1 58.062-133.777-128.066 POINT 2 58.941-132.627-127.572 MODEL 10 POINT 1 100.248 -69.903 -44.772 POINT 2 101.094 -68.717 -44.302 MODEL 11 POINT 1 85.862-111.032 -75.056 POINT 2 86.702-109.839 -74.595 MODEL 12 POINT 1 122.761-144.600-155.931 POINT 2 123.605-143.435-155.407 MODEL 13 POINT 1 55.507-159.304-144.210 POINT 2 56.330-158.122-143.695 MODEL 14 POINT 1 182.752-119.272 -42.608 POINT 2 183.628-118.116 -42.119 MODEL 15 POINT 1 23.163 -99.102 -83.197 POINT 2 23.996 -97.904 -82.736 MODEL 16 POINT 1 149.021 2.178-145.693 POINT 2 149.835 3.390-145.232 MODEL 17 POINT 1 157.790 -18.122 -3.956 POINT 2 158.543 -16.907 -3.411 MODEL 18 POINT 1 52.592-132.081-125.276 POINT 2 53.433-130.912-124.761 MODEL 19 POINT 1 135.278-146.395-144.650 POINT 2 136.055-145.182-144.137 MODEL 20 POINT 1 47.053 -87.306-141.500 POINT 2 47.838 -86.083-141.023 MODEL 21 POINT 1 11.663 -99.070-110.377 POINT 2 12.502 -97.927-109.803 MODEL 22 POINT 1 -80.370-108.121-127.948 POINT 2 -79.581-106.903-127.462 MODEL 23 POINT 1 70.447 -54.021-120.622 POINT 2 71.205 -52.804-120.088 MODEL 24 POINT 1 148.403 -31.319-167.753 POINT 2 149.286 -30.190-167.216 MODEL 25 POINT 1 98.055-150.262 -90.336 POINT 2 98.862-149.055 -89.855 MODEL 26 POINT 1 112.470-112.348-146.659 POINT 2 113.290-111.133-146.219 MODEL 27 POINT 1 -33.125-104.729-100.761 POINT 2 -32.274-103.553-100.280 MODEL 28 POINT 1 87.662 -73.195-244.709 POINT 2 88.501 -72.030-244.182 MODEL 29 POINT 1 140.745-150.196-100.370 POINT 2 141.535-148.971 -99.911 MODEL 30 POINT 1 165.441 -83.229-122.174 POINT 2 166.286 -82.025-121.755 MODEL 31 POINT 1 96.765-106.457 -44.970 POINT 2 97.614-105.317 -44.403 MODEL 32 POINT 1 12.253-144.668-136.369 POINT 2 13.050-143.478-135.830 MODEL 33 POINT 1 47.781 -42.567 26.591 POINT 2 48.646 -41.423 27.123 MODEL 34 POINT 1 16.808-181.697 -62.671 POINT 2 17.631-180.515 -62.158
NMR ensembleConformers calculated total number: 34 / Conformers submitted total number: 34

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