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- PDB-4iwr: C.Esp1396I bound to a 25 base pair operator site -

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Basic information

Entry
Database: PDB / ID: 4iwr
TitleC.Esp1396I bound to a 25 base pair operator site
Components
  • (DNA (25-MER)) x 2
  • Regulatory proteinRegulation of gene expression
KeywordsTRANSCRIPTION/DNA / Restriction-modification / helix-turn-helix / transcriptional regulation / DNA / TRANSCRIPTION-DNA complex
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
DNA / DNA (> 10) / Regulatory protein
Similarity search - Component
Biological speciesEnterobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsMartin, R.N.A. / McGeehan, J.E. / Ball, N.J. / Streeter, S.D. / Thresh, S.-J. / Kneale, G.G.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I.
Authors: Martin, R.N. / McGeehan, J.E. / Ball, N.J. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G.
#1: 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.
#2: 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.
#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: To Be Published
History
DepositionJan 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 (25-MER)
D: DNA (25-MER)
E: Regulatory protein
F: Regulatory protein
G: DNA (25-MER)
H: DNA (25-MER)


Theoretical massNumber of molelcules
Total (without water)68,7938
Polymers68,7938
Non-polymers00
Water41423
1
A: Regulatory protein
B: Regulatory protein
C: DNA (25-MER)
D: DNA (25-MER)


Theoretical massNumber of molelcules
Total (without water)34,3964
Polymers34,3964
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-44 kcal/mol
Surface area14240 Å2
MethodPISA
2
E: Regulatory protein
F: Regulatory protein
G: DNA (25-MER)
H: DNA (25-MER)


Theoretical massNumber of molelcules
Total (without water)34,3964
Polymers34,3964
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-46 kcal/mol
Surface area14340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.020, 48.020, 218.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Regulatory protein / Regulation of gene expression


Mass: 9521.175 Da / Num. of mol.: 4
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 (25-MER)


Mass: 7718.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 25 base pair operator (OL)
#3: DNA chain DNA (25-MER)


Mass: 7634.976 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 25 base pair operator (OL) (complimentary strand)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M PCB buffer, 20 % v/v PEG 1500, 10 mM spermidine , pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2008
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→38.863 Å / Num. obs: 21045 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 59.528 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.49
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.4-2.50.5421.464391213485.4
2.5-2.60.3992.244781204194.4
2.6-2.80.273.458335334397
2.8-30.1835.246816253697.2
3-3.40.07312.5210006344097.7
3.4-3.60.05220.123739118797.6
3.6-3.80.04722.79311393897.9
3.8-40.04724.7291782497.7
4-50.03829.068372223897.7
5-60.03330.884115102897.1
6-70.03130.68197949895.6
7-80.02735.86112928395
8-100.02537.61105226895
10-150.02436.4476920394.9
150.03136.082918481.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.2 Å41.59 Å
Translation4.2 Å41.59 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3S8Q

3s8q


Resolution: 2.4→38.86 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.2534 / WRfactor Rwork: 0.1912 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7826 / SU B: 26.222 / SU ML: 0.274 / SU R Cruickshank DPI: 0.7697 / SU Rfree: 0.3069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.77 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 1069 5.1 %RANDOM
Rwork0.1972 ---
obs0.2002 21041 95.8 %-
all-21045 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.46 Å2 / Biso mean: 67.385 Å2 / Biso min: 6.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.42 Å2-0 Å2
2--0.42 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 2050 0 23 4531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0154780
X-RAY DIFFRACTIONr_bond_other_d0.0020.023727
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.5836846
X-RAY DIFFRACTIONr_angle_other_deg1.16838686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8165300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80524.455101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36515557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3251516
X-RAY DIFFRACTIONr_chiral_restr0.0920.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023813
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02981
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 62 -
Rwork0.292 1211 -
all-1273 -
obs--82.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.96880.82982.46671.75840.0354.6303-0.3263-0.044-0.16480.24820.0059-0.3237-0.38410.43270.32030.2173-0.0957-0.05360.11240.03020.49864.4914.944-16.334
22.7108-0.66851.82741.9125-1.03873.8443-0.5692-0.06960.15110.1419-0.0032-0.2387-0.60860.32520.57250.2133-0.0863-0.03950.11930.04670.483264.0466.344-16.658
35.8460.45212.34243.4961-1.52552.8502-0.06590.0464-0.6496-0.29150.10830.09220.5957-0.4923-0.04240.3295-0.26860.04090.2325-0.06460.67847.084-9.099-25.35
45.96951.88850.56963.5112-0.2653.3226-0.0879-0.2757-1.01380.2155-0.214-0.07110.61850.55020.30190.25530.09710.09140.11680.1220.733464.998-10.075-15.433
52.4481-1.53771.36945.481-2.29795.6791-0.10170.48290.23510.0531-0.28890.29-0.73240.18480.39060.242-0.0805-0.05030.1360.02890.53768.0572.89515.174
63.1721-1.07982.16482.3293-1.47245.6882-0.17290.31940.3780.1411-0.4873-0.0697-0.72910.30770.66020.2267-0.0919-0.05150.14010.00530.50369.533.19715.475
74.2259-1.03451.88623.5806-2.04074.81650.1848-0.1133-0.45520.1261-0.10030.43841.1397-0.5073-0.08460.473-0.21610.05480.1003-0.01370.65264.591-19.21424.185
82.1743-0.60740.60528.91990.87336.9822-0.14020.1597-0.3148-0.2566-0.17891.0043-0.1311-1.23830.31910.0337-0.0143-0.04960.2889-0.10850.720154.815-4.16514.259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 25
2X-RAY DIFFRACTION2D1 - 25
3X-RAY DIFFRACTION3A2 - 76
4X-RAY DIFFRACTION4B2 - 77
5X-RAY DIFFRACTION5G1 - 25
6X-RAY DIFFRACTION6H1 - 25
7X-RAY DIFFRACTION7E2 - 76
8X-RAY DIFFRACTION8F2 - 77

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