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- PDB-1fip: THE STRUCTURE OF FIS MUTANT PRO61ALA ILLUSTRATES THAT THE KINK WI... -

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Basic information

Entry
Database: PDB / ID: 1fip
TitleTHE STRUCTURE OF FIS MUTANT PRO61ALA ILLUSTRATES THAT THE KINK WITHIN THE LONG ALPHA-HELIX IS NOT DUE TO THE PRESENCE OF THE PROLINE RESIDUE
Components
  • FACTOR FOR INVERSION STIMULATION (FIS)
  • UNKNOWN PEPTIDE, POSSIBLY PART OF THE UNOBSERVED RESIDUES IN ENTITY 1
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-binding transcription factor activity / 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 / DNA-binding protein Fis
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsYuan, H.S. / Wang, S.S. / Yang, W.-Z. / Finkel, S.E. / Johnson, R.C.
CitationJournal: J.Biol.Chem. / Year: 1994
Title: The structure of Fis mutant Pro61Ala illustrates that the kink within the long alpha-helix is not due to the presence of the proline residue.
Authors: Yuan, H.S. / Wang, S.S. / Yang, W.Z. / Finkel, S.E. / Johnson, R.C.
History
DepositionSep 26, 1994Processing site: BNL
Revision 1.0Feb 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 5, 2015Group: Structure summary
Revision 1.4Feb 7, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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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)
C: UNKNOWN PEPTIDE, POSSIBLY PART OF THE UNOBSERVED RESIDUES IN ENTITY 1
D: UNKNOWN PEPTIDE, POSSIBLY PART OF THE UNOBSERVED RESIDUES IN ENTITY 1


Theoretical massNumber of molelcules
Total (without water)23,1714
Polymers23,1714
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-38 kcal/mol
Surface area8040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.080, 51.120, 47.290
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: 11226.881 Da / Num. of mol.: 2 / Mutation: P61A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FIS / Gene (production host): FIS / References: UniProt: P11028, UniProt: P0A6R3*PLUS
#2: Protein/peptide UNKNOWN PEPTIDE, POSSIBLY PART OF THE UNOBSERVED RESIDUES IN ENTITY 1


Mass: 358.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
20.5 M1dropNaCl
310 mMTris-HCl1drop
41 M1drop(NH4)2HPO4
52.0 M1reservoir(NH4)2HPO4

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 14501 / % possible obs: 92.5 % / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 14082 / Num. measured all: 47664 / Rmerge(I) obs: 0.0417

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→8 Å / σ(F): 2
Details: THE EXTENDED REGIONS, RESIDUES A 43 - A 46, B 43 - B 46, ARE ILL-DEFINED AND THE ATOMS HAVE HIGH TEMPERATURE FACTORS.
RfactorNum. reflection% reflection
Rwork0.199 --
obs0.199 13428 85.7 %
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 0 74 1286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.19
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.54
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.199 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 3.221

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