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- PDB-4i6u: Crystal Structure of a Y37F mutant of the Restriction-Modificatio... -

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Basic information

Entry
Database: PDB / ID: 4i6u
TitleCrystal Structure of a Y37F mutant of the Restriction-Modification Controller Protein C.Esp1396I
ComponentsRegulatory proteinRegulation of gene expression
KeywordsTRANSCRIPTION / Restriction-modification / helix-turn-helix / transcriptional regulato / DNA
Function / homology
Function and homology information


Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Regulatory protein
Similarity search - Component
Biological speciesEnterobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the restriction-modification controller protein C.Esp1396I.
Authors: Ball, N. / Streeter, S.D. / Kneale, G.G. / McGeehan, J.E.
#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.
#3: Journal: Nucleic Acids Res. / Year: 2012
Title: The structural basis of differential DNA sequence recognition by restriction-modification controller proteins.
Authors: Ball, N.J. / McGeehan, J.E. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the restriction-modification controller protein C.Esp1396I.
Authors: Ball, N. / Streeter, S.D. / Kneale, G.G. / McGeehan, J.E.
History
DepositionNov 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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
E: Regulatory protein
F: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,62814
Polymers57,0316
Non-polymers5978
Water2,648147
1
A: Regulatory protein
D: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4568
Polymers19,0102
Non-polymers4456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-22 kcal/mol
Surface area8580 Å2
MethodPISA
2
B: Regulatory protein
C: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0693
Polymers19,0102
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-20 kcal/mol
Surface area7940 Å2
MethodPISA
3
E: Regulatory protein
F: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1023
Polymers19,0102
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-20 kcal/mol
Surface area8190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.610, 81.850, 135.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Regulatory protein / Regulation of gene expression


Mass: 9505.175 Da / Num. of mol.: 6 / Mutation: Y37F
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

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Non-polymers , 5 types, 155 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M sodium sulphate, 0.2 M sodium acetate, 0.1 M Bis Tris propane, 20 % w/v PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 15, 2012
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.97→45.74 Å / Num. all: 527601 / Num. obs: 38881 / Rmerge(I) obs: 0.081 / Net I/σ(I): 22.6

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimlessdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→41.79 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.063 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 1951 5 %RANDOM
Rwork0.1709 ---
obs0.1732 38823 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.08 Å2 / Biso mean: 23.0441 Å2 / Biso min: 9.35 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.97→41.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3757 0 39 147 3943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193871
X-RAY DIFFRACTIONr_bond_other_d0.0020.024053
X-RAY DIFFRACTIONr_angle_refined_deg1.8642.0085157
X-RAY DIFFRACTIONr_angle_other_deg0.95839369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0795472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40824.295156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93615865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2671524
X-RAY DIFFRACTIONr_chiral_restr0.1470.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02802
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 147 -
Rwork0.173 2699 -
all-2846 -
obs--99.96 %

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