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- PDB-4ivz: A Y37F mutant of C.Esp1396I bound to its highest affinity operato... -

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Basic information

Entry
Database: PDB / ID: 4ivz
TitleA Y37F mutant of C.Esp1396I bound to its highest affinity operator site OM
Components
  • DNA (5'-D(*AP*TP*GP*TP*AP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*GP*AP*CP*A)-3')
  • DNA (5'-D(*TP*TP*GP*TP*CP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*TP*AP*CP*A)-3')
  • Regulatory protein
KeywordsTRANSCRIPTION/DNA / Restriction-modification / helix-turn-helix / transcriptional regulator / DNA / TRANSCRIPTION-DNA complex
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
DNA / DNA (> 10) / Regulatory protein
Similarity search - Component
Biological speciesEnterobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 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: 2009
Title: Transcription regulation of restriction-modification system Esp1396I.
Authors: Bogdanova, E. / Zakharova, M. / Streeter, S. / Taylor, J. / Heyduk, T. / Kneale, G. / Severinov, K.
#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: 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.
#4: 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.
History
DepositionJan 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: DNA (5'-D(*AP*TP*GP*TP*AP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*GP*AP*CP*A)-3')
D: DNA (5'-D(*TP*TP*GP*TP*CP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*TP*AP*CP*A)-3')
E: Regulatory protein
F: Regulatory protein
G: DNA (5'-D(*AP*TP*GP*TP*AP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*GP*AP*CP*A)-3')
H: DNA (5'-D(*TP*TP*GP*TP*CP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*TP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)61,3168
Polymers61,3168
Non-polymers00
Water362
1
A: Regulatory protein
B: Regulatory protein
C: DNA (5'-D(*AP*TP*GP*TP*AP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*GP*AP*CP*A)-3')
D: DNA (5'-D(*TP*TP*GP*TP*CP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*TP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)30,6584
Polymers30,6584
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-45 kcal/mol
Surface area12310 Å2
MethodPISA
2
E: Regulatory protein
F: Regulatory protein
G: DNA (5'-D(*AP*TP*GP*TP*AP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*GP*AP*CP*A)-3')
H: DNA (5'-D(*TP*TP*GP*TP*CP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*TP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)30,6584
Polymers30,6584
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-47 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.540, 146.700, 47.790
Angle α, β, γ (deg.)90.00, 93.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Regulatory protein


Mass: 9505.175 Da / Num. of mol.: 4 / 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
#2: DNA chain DNA (5'-D(*AP*TP*GP*TP*AP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*GP*AP*CP*A)-3')


Mass: 5852.823 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 19 base OM operator
#3: DNA chain DNA (5'-D(*TP*TP*GP*TP*CP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*TP*AP*CP*A)-3')


Mass: 5794.771 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 19 base OM operator complement
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M SPG buffer, 25 % w/v PEG 1500, 10 uM Spermidine , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2012
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→146.81 Å / Num. all: 11888 / Num. obs: 11810 / % possible obs: 99.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 12.7
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.1 Å45.38 Å
Translation3.1 Å45.38 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.1.26data scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UFD

3ufd


Resolution: 3.1→34.63 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.726 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21478 548 4.6 %RANDOM
Rwork0.16987 ---
obs0.17194 11333 98.61 %-
all-11888 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.261 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å2-0 Å2-0.27 Å2
2--1.5 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 3.1→34.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 1546 0 2 4030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0164235
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.6375997
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3315301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06624.356101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.38415565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3441516
X-RAY DIFFRACTIONr_chiral_restr0.1020.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022500
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.087→3.167 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 40 -
Rwork0.151 753 -
obs--86.29 %

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