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- PDB-1ig6: HUMAN MRF-2 DOMAIN, NMR, 11 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1ig6
TitleHUMAN MRF-2 DOMAIN, NMR, 11 STRUCTURES
ComponentsMODULATOR RECOGNITION FACTOR 2
KeywordsDNA BINDING PROTEIN / MRF-2 / DNA-BINDING MOTIF / PROTEIN-DNA INTERACTION
Function / homology
Function and homology information


muscle organ morphogenesis / cell development / fibroblast migration / skeletal system morphogenesis / face morphogenesis / fat pad development / adrenal gland development / female gonad development / roof of mouth development / fat cell differentiation ...muscle organ morphogenesis / cell development / fibroblast migration / skeletal system morphogenesis / face morphogenesis / fat pad development / adrenal gland development / female gonad development / roof of mouth development / fat cell differentiation / platelet-derived growth factor receptor signaling pathway / adipose tissue development / post-embryonic development / liver development / cellular response to leukemia inhibitory factor / kidney development / HDMs demethylate histones / multicellular organism growth / positive regulation of DNA-binding transcription factor activity / male gonad development / transcription coactivator activity / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
AT-rich interactive domain-containing protein 5B / ARID DNA-binding domain / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
AT-rich interactive domain-containing protein 5B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLin, D. / Tsui, V. / Case, D. / Yuan, Y.C. / Chen, Y.
Citation
Journal: To be Published
Title: HUMAN MRF-2 DOMAIN, NMR, 11 STRUCTURES
Authors: Lin, D. / Tsui, V. / Case, D. / Yuan, Y.C. / Chen, Y.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: A Novel DNA-Binding Motif Shares Structural Homology to DNA Replication and Repair Nucleases and Polymerases
Authors: Yuan, Y.C. / Whitson, R.H. / Liu, Q. / Itakura, K. / Chen, Y.
#2: Journal: J.Biomol.NMR / Year: 1998
Title: Resonance Assignments of the MRF-2 DNA-Binding Domain
Authors: Yuan, Y.C. / Whitson, R.H. / Itakura, K. / Chen, Y.
History
DepositionApr 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2001Provider: repository / Type: Initial release
SupersessionMay 2, 2001ID: 1BMY
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MODULATOR RECOGNITION FACTOR 2


Theoretical massNumber of molelcules
Total (without water)12,6531
Polymers12,6531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein MODULATOR RECOGNITION FACTOR 2 / MRF-2


Mass: 12652.646 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRF-2 / Plasmid: PQE30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q14865

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2123D 13C-separated NOESY
1213D 15N-separated NOESY
1313D HNHB
1413D 15N TOCSY-HSQC
2523D (H)CCH-TOCSY
1612D PFG-SE-IPAP
NMR detailsText: This structure was determined using the restraints derived from NMR experiments (NOE, dihedral angles, hydrogen bonds, residual dipolar coupling constants, etc.)

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM MRF-2 U-15N,13C, 100mM PHOSPHATE BUFFER NA, 0.02% NAN3, 5 mM DDT90% H2O/10% D2O
20.7 mM MRF-2 U-15N,13C, 100mM PHOSPHATE BUFFER NA, 0.02% NAN3, 5 mM DDT100% D2O
Sample conditionsIonic strength: 100 mM Sodium Phosphate / pH: 6.00 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix98Biosym/MSIprocessing
DYANA1.5Peter Guntert, et al.structure solution
Amber7Kollman, Case, Merz, Cheatham, Simmerling, Pearlmanrefinement
VNMR6.1Varian Associates INCcollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 2478 restraints, 2290 are NOE-derived distance constraints, 74 dihedral angle restraints, 42 distance restraints from hydrogen bonds, 35 residual ...Details: The structures are based on a total of 2478 restraints, 2290 are NOE-derived distance constraints, 74 dihedral angle restraints, 42 distance restraints from hydrogen bonds, 35 residual dipolar coupling constants.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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