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- PDB-4ia8: Crystal Structure of a Y37A mutant of the Restriction-Modificatio... -

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Basic information

Entry
Database: PDB / ID: 4ia8
TitleCrystal Structure of a Y37A mutant of the Restriction-Modification Controller Protein C.Esp1396I
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 / 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
Biological speciesEnterobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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
DepositionDec 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9543
Polymers18,8582
Non-polymers961
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-28 kcal/mol
Surface area8240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.260, 34.280, 41.120
Angle α, β, γ (deg.)104.440, 108.920, 97.420
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Regulatory protein


Mass: 9429.078 Da / Num. of mol.: 2 / Mutation: A37W
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.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2 M lithium sulfate, 0.1 M sodium acetate, 50 % v/v PEG 400, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917285 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 22, 2011
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917285 Å / Relative weight: 1
ReflectionResolution: 1.85→31.55 Å / Num. all: 19685 / Num. obs: 13243 / % possible obs: 75 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 5.8
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
1.85-1.891.91.5292773379.1
9.06-31.552.11447311595.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.27 Å31.55 Å
Translation4.27 Å31.55 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.1.26data scaling
PHASER2.5.1phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3G5G

3g5g


Resolution: 1.85→31.55 Å / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.885 / SU ML: 0.14 / σ(F): 5.63 / Phase error: 18.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 676 5.29 %
Rwork0.1747 --
obs0.1769 12775 89.65 %
all-19685 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.26 Å2 / Biso mean: 29.4732 Å2 / Biso min: 9.82 Å2
Refinement stepCycle: LAST / Resolution: 1.85→31.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 5 44 1293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181298
X-RAY DIFFRACTIONf_angle_d1.7321744
X-RAY DIFFRACTIONf_chiral_restr0.127210
X-RAY DIFFRACTIONf_plane_restr0.008214
X-RAY DIFFRACTIONf_dihedral_angle_d15.347524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8501-1.99290.1761520.11822489264192
1.9929-2.19340.19461390.12772463260291
2.1934-2.51070.21081490.15922292244186
2.5107-3.16280.23141150.19642489260491
3.1628-32.3180.23541210.19032366248787
Refinement TLS params.Method: refined / Origin x: 11.4798 Å / Origin y: 3.8852 Å / Origin z: 28.8809 Å
111213212223313233
T0.1263 Å20.023 Å20.0238 Å2-0.129 Å20.0319 Å2--0.1152 Å2
L1.677 °21.1874 °21.4791 °2-2.2313 °21.8303 °2--2.1654 °2
S-0.0364 Å °0.0428 Å °0.0934 Å °0.0326 Å °-0.0229 Å °0.0993 Å °-0.0581 Å °-0.0397 Å °0.0536 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 79
2X-RAY DIFFRACTION1allB3 - 79
3X-RAY DIFFRACTION1allB1 - 101
4X-RAY DIFFRACTION1allB1 - 224

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