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- PDB-3ufd: C.Esp1396I bound to its highest affinity operator site OM -

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Basic information

Entry
Database: PDB / ID: 3ufd
TitleC.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 proteinRegulation of gene expression
KeywordsDNA BINDING PROTEIN/DNA / Helix-turn-helix / bacterial gene regulatory protein / DNA BINDING PROTEIN-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. RFL1396 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsBall, N.J. / McGeehan, J.E. / Streeter, S.D. / Thresh, S.-J. / Kneale, G.G.
CitationJournal: 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.
History
DepositionNov 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4159
Polymers61,3808
Non-polymers351
Water23413
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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7255
Polymers30,6904
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-47 kcal/mol
Surface area12220 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)30,6904
Polymers30,6904
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-45 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.490, 147.100, 47.780
Angle α, β, γ (deg.)90.000, 93.680, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31E
41F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A2 - 78
2111B2 - 78
3111E2 - 78
4111F2 - 78

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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. RFL1396 (bacteria) / Gene: esp1396IC / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold / 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: OM 19-mer
#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: OM 19-mer
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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 8.0, 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: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2009
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.7→73.55 Å / Num. all: 17783 / Num. obs: 17783 / % possible obs: 98.9 % / Redundancy: 3.4 % / Rsym value: 0.066 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.853.50.2013.8915726100.20199.7
2.85-3.023.50.154.9870524810.1599.6
3.02-3.233.50.116.4806122980.1199.5
3.23-3.493.50.0699750421550.06999.5
3.49-3.823.50.05810.5687719890.05899.5
3.82-4.273.40.0589.6623018120.05899.4
4.27-4.933.40.0639.4531015630.06398.3
4.93-6.043.20.069.9409813000.0696.1
6.04-8.543.50.0458.9364910440.04599.9
8.54-45.3583.30.04310.417595310.04389.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 33.02 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å45.36 Å
Translation2.7 Å45.36 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→45.36 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.2464 / WRfactor Rwork: 0.2154 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8426 / SU B: 31.762 / SU ML: 0.279 / SU R Cruickshank DPI: 0.3047 / SU Rfree: 0.3502 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 791 5 %RANDOM
Rwork0.2057 ---
obs0.2072 15885 98.71 %-
all-22705 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 61.57 Å2 / Biso mean: 50.88 Å2 / Biso min: 7.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2---0.14 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 1546 1 13 4039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224233
X-RAY DIFFRACTIONr_angle_refined_deg1.522.4475998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7145301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.48624.14199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97315560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0461516
X-RAY DIFFRACTIONr_chiral_restr0.0670.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022498
X-RAY DIFFRACTIONr_mcbond_it0.3591.51509
X-RAY DIFFRACTIONr_mcangle_it0.71922450
X-RAY DIFFRACTIONr_scbond_it1.14632724
X-RAY DIFFRACTIONr_scangle_it1.8974.53548
Refine LS restraints NCS

Ens-ID: 1 / Number: 610 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.020.04
2BTIGHT POSITIONAL0.030.04
3ETIGHT POSITIONAL0.020.04
4FTIGHT POSITIONAL0.030.04
1ATIGHT THERMAL0.060.5
2BTIGHT THERMAL0.060.5
3ETIGHT THERMAL0.050.5
4FTIGHT THERMAL0.060.5
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 42 -
Rwork0.265 1106 -
all-1148 -
obs--99.83 %
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)
11.1355-0.55182.12641.72151.07757.1282-0.0788-0.11060.05310.1725-0.16520.1188-0.0405-0.48020.24390.1363-0.03950.08280.1363-0.02940.093911.7228.2798.805
23.79210.2754-1.69842.11641.99397.4291-0.04480.142-0.1839-0.0233-0.08760.1850.1804-0.43650.13230.1056-0.08830.00260.0866-0.01360.033410.974-1.906-8.887
32.1933-0.467-0.52515.54654.99855.27360.03760.017-0.13530.05280.791-0.5610.08790.5973-0.82860.07210.0027-0.01460.1458-0.04580.220929.4191.4611.185
42.15840.90321.42423.52454.05815.72930.2027-0.04-0.15690.48240.5437-0.51130.5170.4151-0.74640.1750.0215-0.07180.1601-0.05230.146328.898-1.1790.993
59.4788-2.5183-1.30132.1462-0.30893.59250.22460.47260.0465-0.1937-0.14080.2045-0.2697-0.0558-0.08380.09450.0319-0.00760.08190.06320.102-6.59242.8312.179
67.2491-2.58382.20542.52940.62562.70990.33550.6491-0.1135-0.2311-0.1826-0.04570.25450.1984-0.15290.15890.05750.04460.09590.03290.064410.94732.40812.487
74.9831-3.81081.79123.4107-0.98572.1222-0.7845-0.48830.28060.56840.6257-0.1734-0.2276-0.00870.15880.19440.0974-0.03940.23670.05380.10891.89440.22230.247
85.0957-3.1713-0.68013.26580.2642.0206-0.512-0.7067-0.16830.42280.56790.2082-0.0709-0.0853-0.05590.10370.10050.03210.15030.04530.01752.12137.44830.326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 77
2X-RAY DIFFRACTION2B2 - 78
3X-RAY DIFFRACTION3C1 - 19
4X-RAY DIFFRACTION4D1 - 19
5X-RAY DIFFRACTION5E2 - 77
6X-RAY DIFFRACTION6F3 - 78
7X-RAY DIFFRACTION7G1 - 19
8X-RAY DIFFRACTION8H1 - 19

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