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- PDB-2dt5: Crystal Structure of TTHA1657 (AT-rich DNA-binding protein) from ... -

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Basic information

Entry
Database: PDB / ID: 2dt5
TitleCrystal Structure of TTHA1657 (AT-rich DNA-binding protein) from Thermus thermophilus HB8
ComponentsAT-rich DNA-binding protein
KeywordsDNA BINDING PROTEIN / REX / NADH / NAD / ROSSMANN FOLD / REDOX SENSING / WINGED HELIX / THERMUS THEMOPHILUS / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


response to redox state / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Rex DNA-binding, C-terminal domain / Redox-sensing transcriptional repressor Rex / Putative DNA-binding protein N-terminus / CoA binding domain / CoA binding domain / CoA-binding / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / NAD(P)-binding Rossmann-like Domain / Winged helix DNA-binding domain superfamily ...Rex DNA-binding, C-terminal domain / Redox-sensing transcriptional repressor Rex / Putative DNA-binding protein N-terminus / CoA binding domain / CoA binding domain / CoA-binding / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / NAD(P)-binding Rossmann-like Domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Redox-sensing transcriptional repressor Rex
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.16 Å
AuthorsNakamura, A. / Sosa, A. / Komori, H. / Kita, A. / Miki, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of TTHA1657 (AT-rich DNA-binding protein; p25) from Thermus thermophilus HB8 at 2.16 A resolution
Authors: Nakamura, A. / Sosa, A. / Komori, H. / Kita, A. / Miki, K.
History
DepositionJul 11, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: 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: AT-rich DNA-binding protein
B: AT-rich DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,38912
Polymers46,3582
Non-polymers2,03110
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9970 Å2
ΔGint-146 kcal/mol
Surface area19970 Å2
MethodPISA
2
A: AT-rich DNA-binding protein
B: AT-rich DNA-binding protein
hetero molecules

A: AT-rich DNA-binding protein
B: AT-rich DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,77824
Polymers92,7164
Non-polymers4,06220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area22160 Å2
ΔGint-349 kcal/mol
Surface area38080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.595, 135.595, 68.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-709-

HOH

21A-778-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein AT-rich DNA-binding protein / Redox sensing repressor p25


Mass: 23178.994 Da / Num. of mol.: 2 / Mutation: E36G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1657 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHS3

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Non-polymers , 5 types, 302 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: LITHIUM SULFATE, HEPES-NAOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→20 Å / Num. obs: 34573 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.043 / Net I/σ(I): 47.9
Reflection shellResolution: 2.16→2.24 Å / Mean I/σ(I) obs: 8.8 / Rsym value: 0.224 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.16→19.63 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 177972.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1653 5 %RANDOM
Rwork0.195 ---
obs0.195 33150 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.161 Å2 / ksol: 0.373367 e/Å3
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å20 Å20 Å2
2--2.04 Å20 Å2
3----4.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.16→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 125 292 3667
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_mcbond_it3.361.5
X-RAY DIFFRACTIONc_mcangle_it4.142
X-RAY DIFFRACTIONc_scbond_it5.142
X-RAY DIFFRACTIONc_scangle_it6.72.5
LS refinement shellResolution: 2.16→2.24 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.271 145 4.9 %
Rwork0.201 2788 -
obs--86.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4nad.parnad.top
X-RAY DIFFRACTION5gol.pargol.top

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