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- PDB-1etq: THE CRYSTAL STRUCTURE OF E. COLI FIS MUTANT R71Y -

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Basic information

Entry
Database: PDB / ID: 1etq
TitleTHE CRYSTAL STRUCTURE OF E. COLI FIS MUTANT R71Y
ComponentsFACTOR FOR INVERSION STIMULATION
KeywordsTRANSCRIPTION ACTIVATOR / TRANSCRIPTIONAL ACTIVATION REGION / 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: 2.8 Å
AuthorsCheng, Y.S. / Yang, W.Z. / Johnson, R.C. / Yuan, H.S.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structural analysis of the transcriptional activation on Fis: crystal structures of six Fis mutants with different activation properties.
Authors: Cheng, Y.S. / Yang, W.Z. / Johnson, R.C. / Yuan, H.S.
History
DepositionApr 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
Remark 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS THAT GIVE ONE ... THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS THAT GIVE ONE BIOLOGICAL DIMER MOLECULE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FACTOR FOR INVERSION STIMULATION
B: FACTOR FOR INVERSION STIMULATION
C: FACTOR FOR INVERSION STIMULATION
D: FACTOR FOR INVERSION STIMULATION


Theoretical massNumber of molelcules
Total (without water)45,0364
Polymers45,0364
Non-polymers00
Water1,24369
1
A: FACTOR FOR INVERSION STIMULATION
B: FACTOR FOR INVERSION STIMULATION


Theoretical massNumber of molelcules
Total (without water)22,5182
Polymers22,5182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-35 kcal/mol
Surface area8920 Å2
MethodPISA
2
C: FACTOR FOR INVERSION STIMULATION
D: FACTOR FOR INVERSION STIMULATION


Theoretical massNumber of molelcules
Total (without water)22,5182
Polymers22,5182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-36 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.21, 57.97, 135.30
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer constructed from chain A and a symmetry partner (chain B) generated by the non-crystallographic two-fold

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Components

#1: Protein
FACTOR FOR INVERSION STIMULATION / FIS


Mass: 11258.898 Da / Num. of mol.: 4 / Mutation: R71Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (-FIS) / References: UniProt: P0A6R3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMutation at BC turn at the transcriptional activation region.

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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: 2.2 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mg/ml protein, 0.5 M sodium chloride, 0.05 M Na-Hepes(pH7.5), 12.5% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
21 M1dropNaCl
320 mMTris-HCl1drop
40.1 MNa-HEPES1reservoir
525 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 28, 1999 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 61806 / Num. obs: 10232 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 66.4 Å2 / Rsym value: 0.103 / Net I/σ(I): 20.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.97 % / Num. unique all: 999 / Rsym value: 0.51 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 61806 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementStarting model: The wild-type FIS

Resolution: 2.8→19.78 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 228553.11 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1024 10.3 %RANDOM
Rwork0.216 ---
all0.216 10211 --
obs-9915 97 %-
Solvent computationSolvent model: flat model / Bsol: 39.1379 Å2 / ksol: 0.301265 e/Å3
Displacement parametersBiso mean: 50.9 Å2
Baniso -1Baniso -2Baniso -3
1--7.18 Å20 Å20 Å2
2--7.87 Å20 Å2
3----0.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 0 69 2624
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.015
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it2.271.5
X-RAY DIFFRACTIONc_mcangle_it3.862
X-RAY DIFFRACTIONc_scbond_it3.532
X-RAY DIFFRACTIONc_scangle_it5.492.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 159 10.3 %
Rwork0.274 1390 -
obs--93.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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