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- PDB-1f36: THE CRYSTAL STRUCTURE OF FIS MUTANT K36E REVEALS THAT THE TRANSAC... -

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Basic information

Entry
Database: PDB / ID: 1f36
TitleTHE CRYSTAL STRUCTURE OF FIS MUTANT K36E REVEALS THAT THE TRANSACTIVATION REGION OF THE FIS PROTEIN CONTAINS EXTENDED MOBILE BETA-HAIRPIN ARMS
ComponentsFIS
KeywordsTRANSACTIVATION REGION / DNA-BINDING PROTEIN / PROTEIN-PROTEIN INTERACTION DOMAIN
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 / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSafo, M.K. / Yuan, H.S.
CitationJournal: EMBO J. / Year: 1997
Title: The transactivation region of the fis protein that controls site-specific DNA inversion contains extended mobile beta-hairpin arms.
Authors: Safo, M.K. / Yang, W.Z. / Corselli, L. / Cramton, S.E. / Yuan, H.S. / Johnson, R.C.
History
DepositionJun 20, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIS
B: FIS


Theoretical massNumber of molelcules
Total (without water)22,5062
Polymers22,5062
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-34 kcal/mol
Surface area10180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.900, 51.900, 294.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein FIS


Mass: 11252.853 Da / Num. of mol.: 2 / Mutation: K36E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: YMEL / Cell line: BL21 / Gene: FIS / Plasmid: PRJ1296 / Cellular location (production host): NUCLEOID / Gene (production host): FIS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (-FIS) / References: UniProt: P0A6R3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52 %
Description: SEARCH MODEL INCLUDED RESIDUES 24 - 98 OF THE DIMER AND THE CORRESPONDING TETRAPEPTIDE CHAINS (RESIDUES 10 - 13).
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.2
Details: CRYSTALS GROWN BY HANGING DROP VAPOR DIFFUSION FROM A SOLUTION OF 20 MG/ML PROTEIN, 500 MM NACL, 10 MM TRIS-HCL, PH 8.2, 2 M NAFORMATE, AGAINST 4 M NAFORMATE AS THE RESERVOIR, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
22 Msodium formate1drop
34 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 16, 1996 / Details: Y
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 7139 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 54.6 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069
Reflection shellResolution: 2.65→2.75 Å / Redundancy: 2 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 1.63 / % possible all: 55.6
Reflection
*PLUS
Num. measured all: 79532
Reflection shell
*PLUS
% possible obs: 55.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
MSCdata reduction
MSCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ORTHORHOMBIC CRYSTAL FORM OF THE LYS36-GLU FIS STRUCTURE

Resolution: 2.65→8 Å / σ(F): 1
Details: MET A 1 - ASP A 9 ARE DISORDERED IN THE PROTEIN STRUCTURE. MET B 1 - ASP B 9 ARE DISORDERED IN THE PROTEIN STRUCTURE. PREVIOUSLY DISORDERED REGION (RESIDUES 1 - 24) IN ALL THE KNOWN CRYSTAL ...Details: MET A 1 - ASP A 9 ARE DISORDERED IN THE PROTEIN STRUCTURE. MET B 1 - ASP B 9 ARE DISORDERED IN THE PROTEIN STRUCTURE. PREVIOUSLY DISORDERED REGION (RESIDUES 1 - 24) IN ALL THE KNOWN CRYSTAL STRUCTERS OF THE FIS PROTEIN IS NOW PARTLY RESOLVED IN THIS LYS36-GLU FIS MUTANT (RESIDUES 10 - 24) AS BETA HAIRPIN STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 526 8 %RANDOM
Rwork0.222 ---
obs0.222 6577 90.6 %-
Displacement parametersBiso mean: 42.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.52 Å
Refinement stepCycle: LAST / Resolution: 2.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 0 22 1438
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.143
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.72
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.13
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)
11RESTRAINTX-RAY DIFFRACTION1
22X-RAY DIFFRACTION1
LS refinement shellResolution: 2.65→2.77 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.347 35 8 %
Rwork0.312 395 -
obs--50.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.72
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.13
LS refinement shell
*PLUS
Rfactor obs: 0.312

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