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- PDB-1etw: THE CRYSTAL STRUCTURE OF E. COLI FIS MUTANT G72D -

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Basic information

Entry
Database: PDB / ID: 1etw
TitleTHE CRYSTAL STRUCTURE OF E. COLI FIS MUTANT G72D
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 / 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 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


Theoretical massNumber of molelcules
Total (without water)22,6222
Polymers22,6222
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-36 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.33, 50.26, 47.26
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: 11310.953 Da / Num. of mol.: 2 / Mutation: G72D
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


Mass: 18.015 Da / Num. of mol.: 145 / 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 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9 mg/ml protein, 0.5 M sodium chloride, 0.1M magnesium acetate, 0.05M sodium cacodylate(pH 6.5), 10% PEG 8000, 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 Mmagnesium acetate1reservoir
50.1 Msodium cacodylate1reservoir
620 %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: Dec 12, 1998 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 76866 / Num. obs: 12915 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.95 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.055 / Net I/σ(I): 31.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.1 % / Num. unique all: 1252 / Rsym value: 0.301 / % possible all: 98.9
Reflection
*PLUS
Num. measured all: 76866 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 98.9 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 6.1

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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→19.23 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 498944.02 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1296 10.3 %RANDOM
Rwork0.231 ---
all0.231 12956 --
obs-12610 97.2 %-
Solvent computationSolvent model: flat model / Bsol: 50.414 Å2 / ksol: 0.325262 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20 Å2
2---2.84 Å20 Å2
3---1.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2→19.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 0 145 1465
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.023
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 201 10 %
Rwork0.239 1801 -
obs--95.3 %
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_deg18.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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