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- PDB-3fis: THE MOLECULAR STRUCTURE OF WILD-TYPE AND A MUTANT FIS PROTEIN: RE... -

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Basic information

Entry
Database: PDB / ID: 3fis
TitleTHE MOLECULAR STRUCTURE OF WILD-TYPE AND A MUTANT FIS PROTEIN: RELATIONSHIP BETWEEN MUTATIONAL CHANGES AND RECOMBINATIONAL ENHANCER FUNCTION OR DNA BINDING
ComponentsFACTOR FOR INVERSION STIMULATION (FIS)
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN
Function / homology
Function and homology information


invertasome / positive regulation of DNA recombination / sequence-specific DNA binding, bending / provirus excision / nucleoid / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / chromosome organization / core promoter sequence-specific DNA binding / response to radiation ...invertasome / positive regulation of DNA recombination / sequence-specific DNA binding, bending / provirus excision / nucleoid / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / chromosome organization / core promoter sequence-specific DNA binding / response to radiation / protein-DNA complex / nucleosome / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / cytosol
Similarity search - Function
DNA-binding protein Fis / : / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-binding protein Fis
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsYuan, H.S. / Finkel, S.E. / Feng, J-A. / Johnson, R.C. / Dickerson, R.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: The molecular structure of wild-type and a mutant Fis protein: relationship between mutational changes and recombinational enhancer function or DNA binding.
Authors: Yuan, H.S. / Finkel, S.E. / Feng, J.A. / Kaczor-Grzeskowiak, M. / Johnson, R.C. / Dickerson, R.E.
History
DepositionAug 12, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_keywords.text
Remark 650HELIX THE EXTENDED REGIONS BEFORE A-HELIX (RESIDUES A 20 TO A 25 AND B 20 TO B 25) AND AFTER A- ...HELIX THE EXTENDED REGIONS BEFORE A-HELIX (RESIDUES A 20 TO A 25 AND B 20 TO B 25) AND AFTER A-HELIX (RESIDUES A 43 TO A 46 AND B 43 TO B 46) ARE MORE FLEXIBLE. THE STRUCTURE IN THESE REGIONS IS ILL-DEFINED AND THE ATOMS HAVE HIGH TEMPERATURE FACTORS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FACTOR FOR INVERSION STIMULATION (FIS)
B: FACTOR FOR INVERSION STIMULATION (FIS)


Theoretical massNumber of molelcules
Total (without water)22,5062
Polymers22,5062
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-28 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.400, 50.900, 47.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FACTOR FOR INVERSION STIMULATION (FIS)


Mass: 11252.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FIS / Gene (production host): FIS / References: UniProt: P0A6R3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
118 mg/mlprotein1drop
21 M1dropNaCl
320 mMTris-HCl1drop
450 mM2-mercaptoethanol1drop
51.3 Mammonium phosphate1reservoircan be replaced with PEG400

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Data collection

Reflection
*PLUS
Highest resolution: 2.25 Å / Num. obs: 6451 / % possible obs: 68 % / Num. measured all: 30267 / Rmerge(I) obs: 0.0323

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.183 / Rfactor obs: 0.183 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 0 0 29 1203
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 6053 / σ(F): 2 / Rfactor obs: 0.183 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg3.6

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