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- PDB-1fia: CRYSTAL STRUCTURE OF THE FACTOR FOR INVERSION STIMULATION FIS AT ... -

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Basic information

Entry
Database: PDB / ID: 1fia
TitleCRYSTAL STRUCTURE OF THE FACTOR FOR INVERSION STIMULATION FIS AT 2.0 ANGSTROMS RESOLUTION
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 / protein-DNA complex ...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 / protein-DNA complex / response to radiation / 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 Å
AuthorsKostrewa, D. / Granzin, J. / Choe, H.-W. / Labahn, J. / Saenger, W.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Crystal structure of the factor for inversion stimulation FIS at 2.0 A resolution.
Authors: Kostrewa, D. / Granzin, J. / Stock, D. / Choe, H.W. / Labahn, J. / Saenger, W.
#1: Journal: Nature / Year: 1991
Title: Three-Dimensional Structure of the E. Coli DNA-Binding Protein FIS
Authors: Kostrewa, D. / Granzin, J. / Koch, C. / Choe, H.-W. / Raghunathan, S. / Wolf, W. / Labahn, J. / Kahmann, R. / Saenger, W.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallization of the DNA-Binding Escherichia Coli Protein FIS
Authors: Choe, H.-W. / Labahn, J. / Itoh, S. / Koch, C. / Kahmann, R. / Saenger, W.
History
DepositionDec 18, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Structure summary
Category: pdbx_database_status / struct_conf ...pdbx_database_status / struct_conf / struct_conf_type / struct_keywords
Item: _pdbx_database_status.process_site / _struct_keywords.text
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-43 kcal/mol
Surface area8750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.390, 50.980, 79.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES VAL 10 AND LYS 25 IN BOTH CHAINS WERE MODELLED AS ALANINE.

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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.: 82 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHELICES C AND D OF EACH CHAIN FORM THE HELIX-TURN-HELIX MOTIF FOR DNA BINDING.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-30 mg/mlFIS1drop
20.5 M1dropNaCl
31 mM1dropNaN3
410 mMTris-HCl1drop
51.5 Msodium/potassium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. all: 12719 / Num. obs: 8221 / % possible obs: 92 % / Num. measured all: 44050

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.192 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 0 82 1341
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg1.7
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Num. reflection all: 12719
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_deg22.5
X-RAY DIFFRACTIONt_plane_restr0.006

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