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- PDB-1p7a: Solution Structure of the Third Zinc Finger from BKLF -

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Basic information

Entry
Database: PDB / ID: 1p7a
TitleSolution Structure of the Third Zinc Finger from BKLF
ComponentsKruppel-like factor 3
KeywordsDNA BINDING PROTEIN / CLASSICAL ZINC FINGER / KRUPPEL-LIKE / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


cellular response to peptide / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding
Similarity search - Function
Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Krueppel-like factor 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, molecular dynamics torsion angle dynamics
AuthorsSimpson, R.J.Y. / Cram, E.D. / Czolij, R. / Matthews, J.M. / Crossley, M. / Mackay, J.P.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: CCHX zinc finger derivatives retain the ability to bind Zn(II) and mediate protein-DNA interactions.
Authors: Simpson, R.J. / Cram, E.D. / Czolij, R. / Matthews, J.M. / Crossley, M. / Mackay, J.P.
History
DepositionApr 30, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2016Group: Structure summary
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_struct_conn_angle / 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_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kruppel-like factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2732
Polymers4,2081
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 35structures with the lowest energy
Representative

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Components

#1: Protein/peptide Kruppel-like factor 3 / BF3 / BKLF


Mass: 4207.827 Da / Num. of mol.: 1 / Fragment: residues 9-37
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: BKLF / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q60980
#2: 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 experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
242HNHA
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM BF3; 4.5mM TCEP; 4.5mM ZnSO490% H2O/10% D2O
21mM BF3 U-15N; 1.5mM TCEP; 1.5mM ZnSO490% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15.5 ambient 280 K
25.5 ambient 280 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukerprocessing
DYANA1.5structure solution
XEASY1.3.13Bartels et aldata analysis
ARIA1.1.2Linge et alrefinement
ARIA1.1.2Linge et alstructure solution
RefinementMethod: simulated annealing, molecular dynamics torsion angle dynamics
Software ordinal: 1
Details: Structure calculations were performed using the package ARIA 1.1 (Ambiguous Restraints in Iterative Assignment)> Final structures are based on 719 unambiguous NOE-derived distance ...Details: Structure calculations were performed using the package ARIA 1.1 (Ambiguous Restraints in Iterative Assignment)> Final structures are based on 719 unambiguous NOE-derived distance consraints, 6 sets of ambiguous NOE-derived distance constraints and 28 additional dihedral angle restraints.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 35 / Conformers submitted total number: 20

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