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- PDB-1fse: CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS REGULATORY PROTEIN GERE -

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Basic information

Entry
Database: PDB / ID: 1fse
TitleCRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS REGULATORY PROTEIN GERE
ComponentsGERE
KeywordsTRANSCRIPTION / Helix-turn-helix DNA-binding protein transcriptional regulator
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Spore germination protein GerE
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsDucros, V.M.-A. / Lewis, R.J. / Verma, C.S. / Dodson, E.J. / Leonard, G. / Turkenburg, J.P. / Murshudov, G.N. / Wilkinson, A.J. / Brannigan, J.A.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis.
Authors: Ducros, V.M. / Lewis, R.J. / Verma, C.S. / Dodson, E.J. / Leonard, G. / Turkenburg, J.P. / Murshudov, G.N. / Wilkinson, A.J. / Brannigan, J.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Bacillus subtilis regulatory protein GerE
Authors: Ducros, V. / Brannigan, J.A. / Lewis, R.J. / Wilkinson, A.J.
History
DepositionSep 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GERE
B: GERE
C: GERE
D: GERE
E: GERE
F: GERE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,27913
Polymers51,6186
Non-polymers6617
Water5,801322
1
A: GERE
B: GERE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2983
Polymers17,2062
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: GERE
F: GERE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4905
Polymers17,2062
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: GERE
E: GERE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4905
Polymers17,2062
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-29 kcal/mol
Surface area7630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.019, 61.749, 71.743
Angle α, β, γ (deg.)90.00, 97.08, 90.00
Int Tables number5
Space group name H-MC121
DetailsThere six monomers in the asymmetric unit arranged as three pairs of dimers (A and B, C and F, D and E)

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Components

#1: Protein
GERE


Mass: 8603.060 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PET26B / Production host: Escherichia coli (E. coli) / References: UniProt: P11470
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.3 Å3/Da / Density % sol: 46.06 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: Peg4000, sodium acetate, lithium or ammonium sulfate, pH 5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 291 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
230 %PEG40001reservoir
30.1 Msodium acetate1reservoir
40.2 Mlithium sulfate1reservoiror ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC / Detector: IMAGE PLATE / Date: Feb 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.05→15 Å / Num. all: 25472 / Num. obs: 25472 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.11 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.53
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 2.83 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.07 / Num. unique all: 2421 / % possible all: 95.5
Reflection
*PLUS
Num. obs: 29311 / Num. measured all: 91541
Reflection shell
*PLUS
% possible obs: 95.5 %

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.05→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Used Translation, Libration and Screw motion (TLS) approach to refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1492 5 %random
Rwork0.214 ---
obs-29616 99 %-
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3060 0 38 322 3420
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.022
X-RAY DIFFRACTIONp_angle_d1.562.007

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