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- PDB-4fbi: Crystal Structure of an R46A mutant of the Restriction-Modificati... -

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Basic information

Entry
Database: PDB / ID: 4fbi
TitleCrystal Structure of an R46A mutant of the Restriction-Modification Controller Protein C.Esp1396I (Trigonal Form)
ComponentsRegulatory protein
KeywordsTRANSCRIPTION / Restriction-modification / helix-turn-helix / transcriptional regulator / DNA
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
: / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsMartin, R.N.A. / McGeehan, J.E. / Kneale, G.G.
Citation
Journal: Plos One / Year: 2014
Title: Structural and Mutagenic Analysis of the RM Controller Protein C.Esp1396I.
Authors: Martin, R.N. / McGeehan, J.E. / Kneale, G.
#1: Journal: Nucleic Acids Res. / Year: 2008
Title: Structural analysis of the genetic switch that regulates the expression of restriction-modification genes.
Authors: McGeehan, J.E. / Streeter, S.D. / Thresh, S.J. / Ball, N. / Ravelli, R.B. / Kneale, G.G.
#2: Journal: Nucleic Acids Res. / Year: 2012
Title: Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex.
Authors: McGeehan, J.E. / Ball, N.J. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G.
History
DepositionMay 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Other
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Regulatory protein
B: Regulatory protein
C: Regulatory protein
D: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9246
Polymers37,7404
Non-polymers1842
Water4,576254
1
A: Regulatory protein
B: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9623
Polymers18,8702
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-20 kcal/mol
Surface area7820 Å2
MethodPISA
2
C: Regulatory protein
D: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9623
Polymers18,8702
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-21 kcal/mol
Surface area7790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.329, 65.329, 71.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Regulatory protein


Mass: 9435.059 Da / Num. of mol.: 4 / Mutation: R46A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter sp. (bacteria) / Strain: RFL1396 / Gene: esp1396IC / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8GGH0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M MIB buffer, 25% w/v PEG 1500, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979494 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2011
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979494 Å / Relative weight: 1
ReflectionResolution: 1.487→71.38 Å / Num. all: 53279 / Num. obs: 53279 / % possible obs: 95.1 % / Redundancy: 2.4 % / Rsym value: 0.034 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.49-1.572.40.24631901179280.24697
1.57-1.662.20.1774.21567970100.17791
1.66-1.782.40.1246.11678170840.12497.3
1.78-1.922.50.0839.11675966870.08398.1
1.92-2.12.50.05213.41493760110.05296.4
2.1-2.352.20.03519.31104150190.03589.6
2.35-2.712.50.02923.41193148000.02996.6
2.71-3.332.60.02426.11059741180.02497.9
3.33-4.72.40.01930.7673028440.01988.1
4.7-30.1862.80.02123.6506717780.02199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.19 Å
Translation2.5 Å30.19 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.2.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→30.19 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1939 / WRfactor Rwork: 0.1566 / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.8951 / SU B: 0.003 / SU ML: 0 / SU R Cruickshank DPI: 0.0699 / SU Rfree: 0.0761 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1989 2638 5.1 %RANDOM
Rwork0.16 ---
obs0.1619 51880 95.01 %-
all-53279 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.27 Å2 / Biso mean: 16.4158 Å2 / Biso min: 5.29 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 12 254 2701
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.028
X-RAY DIFFRACTIONr_angle_refined_deg2.889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21
X-RAY DIFFRACTIONr_chiral_restr0.185
X-RAY DIFFRACTIONr_gen_planes_refined0.014
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.195
X-RAY DIFFRACTIONr_mcbond_it2.885
X-RAY DIFFRACTIONr_mcangle_it4.03
X-RAY DIFFRACTIONr_scbond_it6.844
X-RAY DIFFRACTIONr_scangle_it6.359
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 221 -
Rwork0.221 3713 -
all-3934 -
obs--97.45 %

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