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- PDB-4f8d: Crystal Structure of an R46A mutant of the Restriction-Modificati... -

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Basic information

Entry
Database: PDB / ID: 4f8d
TitleCrystal Structure of an R46A mutant of the Restriction-Modification Controller Protein C.Esp1396I (Monoclinic 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: 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.
#3: 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 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein
B: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3008
Polymers18,8702
Non-polymers4306
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-82 kcal/mol
Surface area9230 Å2
MethodPISA
2
B: Regulatory protein
hetero molecules

A: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3008
Polymers18,8702
Non-polymers4306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area1200 Å2
ΔGint-80 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.400, 51.000, 74.600
Angle α, β, γ (deg.)90.000, 96.600, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Regulatory protein


Mass: 9435.059 Da / Num. of mol.: 2 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 200mM Sodium Sulphate, 20% PEG 3350, pH 7.8, VAPOR DIFFUSION, SITTING 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: 1.5→24.7 Å / Num. all: 90345 / Num. obs: 27204 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.014 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.31
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.60.4043.02124314603194.9
1.6-1.80.2484.97190926625197.6
1.8-20.1189.74128854285198.7
2-30.03923.3262488219199.3
3-40.02236.1964552025199.3
4-50.01844.812420727198.1
5-60.01742.861035315199.7
6-80.01742.09850259197.4
8-100.01344.4923777181.9
10-200.01539.3318063168.5
20-300.01638.97176154.5
1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→24.7 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1929 / WRfactor Rwork: 0.1693 / Occupancy max: 1 / Occupancy min: 0.02 / FOM work R set: 0.8197 / SU B: 1.296 / SU ML: 0.048 / SU R Cruickshank DPI: 0.076 / SU Rfree: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 1377 5.1 %RANDOM
Rwork0.1771 ---
obs0.1783 27185 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.55 Å2 / Biso mean: 18.566 Å2 / Biso min: 6.01 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 22 125 1411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.021433
X-RAY DIFFRACTIONr_angle_refined_deg2.6332.0181947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9625194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.47224.73757
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89415325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.214158
X-RAY DIFFRACTIONr_chiral_restr0.1870.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021008
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 87 -
Rwork0.279 1717 -
all-1804 -
obs--91.71 %

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