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- PDB-3eik: double stranded DNA binding protein -

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Basic information

Entry
Database: PDB / ID: 3eik
Titledouble stranded DNA binding protein
ComponentsTATA-box-binding protein
KeywordsTRANSCRIPTION / TATA box binding protein / DNA-binding / Initiation factor / Nucleus
Function / homology
Function and homology information


DNA-templated transcription initiation / DNA binding / identical protein binding / nucleus
Similarity search - Function
TATA-Binding Protein / TATA-Binding Protein / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TBP domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRANSCRIPTION INITIATION FACTOR TFIID (TFIID-1)
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCui, S. / Wollmann, P. / Moldt, M. / Hopfner, K.-P.
CitationJournal: To be Published
Title: structural studies of ecTBP
Authors: Cui, S. / Wollmann, P. / Moldt, M. / Hopfner, K.-P.
History
DepositionSep 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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

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Assembly

Deposited unit
A: TATA-box-binding protein
B: TATA-box-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3778
Polymers49,0052
Non-polymers3726
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint4.7 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.400, 104.400, 129.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein TATA-box-binding protein


Mass: 24502.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Strain: GB-M1 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q8ST28
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES,2M NaCl,4% Acetone, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 41388 / Num. obs: 37329 / % possible obs: 90.19 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.03 % / Biso Wilson estimate: 25.23 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 2.99 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.44 / Num. unique all: 5640 / Rsym value: 0.326 / % possible all: 84.8

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
remdaq.pilatusdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YTB

1ytb


Resolution: 1.9→26.1 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.851 / SU ML: 0.31 / σ(F): 1.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1950 5.01 %RANDOM
Rwork0.177 ---
obs0.18 36954 94.04 %-
all-38913 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.278 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 68.87 Å2 / Biso mean: 30.794 Å2 / Biso min: 13.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.204 Å20 Å2-0 Å2
2--0.204 Å2-0 Å2
3----0.407 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 24 148 3080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072990
X-RAY DIFFRACTIONf_angle_d1.0294032
X-RAY DIFFRACTIONf_chiral_restr0.071459
X-RAY DIFFRACTIONf_plane_restr0.005510
X-RAY DIFFRACTIONf_dihedral_angle_d16.0411124
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9460.2841280.1882628275693
1.946-1.9990.2791430.1672697284097
1.999-2.0580.2221520.1512703285596
2.058-2.1240.2611430.1542652279594
2.124-2.20.2691250.162636276195
2.2-2.2880.2611730.1632685285896
2.288-2.3920.2711370.1692709284696
2.392-2.5180.2621470.1742630277795
2.518-2.6760.2541530.1732603275693
2.676-2.8820.2361380.1822661279995
2.882-3.1710.2481380.1882640277893
3.171-3.6290.2061230.1752583270692
3.629-4.5690.1921290.1542599272892
4.569-26.1030.1811210.1632537265890

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