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- PDB-4fn3: Crystal Structure of an S52A mutant of the Restriction-Modificati... -

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Basic information

Entry
Database: PDB / ID: 4fn3
TitleCrystal Structure of an S52A 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. RFL1396 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 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.
History
DepositionJun 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 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 / 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)19,2995
Polymers19,0102
Non-polymers2883
Water1,65792
1
A: Regulatory protein
hetero molecules

A: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3956
Polymers19,0102
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area2550 Å2
ΔGint-58 kcal/mol
Surface area8250 Å2
MethodPISA
2
B: Regulatory protein
hetero molecules

B: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2024
Polymers19,0102
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area2400 Å2
ΔGint-43 kcal/mol
Surface area8190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.590, 51.320, 74.380
Angle α, β, γ (deg.)90.000, 95.460, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Regulatory protein


Mass: 9505.175 Da / Num. of mol.: 2 / Mutation: S52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter sp. RFL1396 (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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 47.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 200mM Sodium Sulphate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 6, 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: 1.786→74.043 Å / Num. all: 16667 / Num. obs: 16667 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rsym value: 0.084 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.79-1.8860.4341.51438123850.43499.8
1.88-25.80.3012.11346923060.30199.8
2-2.135.70.1813.51234621700.18199.9
2.13-2.3160.1225.21211520040.12299.8
2.31-2.535.60.161017118300.199.9
2.53-2.826.10.0837.21031416860.08399.9
2.82-3.265.70.0678852814860.067100
3.26-3.996.20.0558.1784212640.05599.8
3.99-5.655.70.0567.756079820.05699.8
5.65-37.0215.90.053832585540.05399.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.02 Å
Translation2.5 Å37.02 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→34.41 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.2143 / WRfactor Rwork: 0.1834 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.7853 / SU B: 2.313 / SU ML: 0.073 / SU R Cruickshank DPI: 0.1254 / SU Rfree: 0.1148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 841 5 %RANDOM
Rwork0.1788 ---
obs0.1802 16665 99.79 %-
all-16667 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.21 Å2 / Biso mean: 18.9933 Å2 / Biso min: 7.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.79→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 15 92 1363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021411
X-RAY DIFFRACTIONr_angle_refined_deg2.1712.0121913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9365194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.34724.57659
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31815319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.932159
X-RAY DIFFRACTIONr_chiral_restr0.1730.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021001
LS refinement shellResolution: 1.786→1.832 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 67 -
Rwork0.253 1131 -
all-1198 -
obs--99.83 %

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