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- PDB-1uso: DCOH, A BIFUNCTIONAL PROTEIN-BINDING TRANSCRIPTIONAL COACTIVATOR,... -

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Basic information

Entry
Database: PDB / ID: 1uso
TitleDCOH, A BIFUNCTIONAL PROTEIN-BINDING TRANSCRIPTIONAL COACTIVATOR, PRO9LEU MUTANT
ComponentsHEPATOCYTE NUCLEAR FACTOR 1-ALPHA
KeywordsTRANSCRIPTIONAL STIMULATOR / DIMERIZATION COFACTOR / DEHYDRATASE / 4A-CARBINOLAMINE DEHYDRATASE / TRANSREGULATOR OF HOMEODOMAIN PROTEINS / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS
Function / homology
Function and homology information


4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / tetrahydrobiopterin biosynthetic process
Similarity search - Function
Transcriptional coactivator/pterin dehydratase / Pterin 4 alpha carbinolamine dehydratase / Pterin 4 alpha carbinolamine dehydratase superfamily / Pterin 4 alpha carbinolamine dehydratase / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4a-hydroxytetrahydrobiopterin dehydratase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsTahirov, T.H. / Inagaki, E.
CitationJournal: To be Published
Title: Crystal Structure of Transcriptional Coactivator DCoH from Thermus Thermophilus
Authors: Tahirov, T.H. / Inagaki, E.
History
DepositionNov 27, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
B: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2735
Polymers18,9852
Non-polymers2883
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.430, 48.687, 94.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HEPATOCYTE NUCLEAR FACTOR 1-ALPHA / DCOH


Mass: 9492.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHC7*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE PROLINE AT POSITION 9 WAS MUTATED TO LEU

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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: 1.68 Å3/Da / Density % sol: 26.2 %
Crystal growMethod: vapor diffusion / pH: 6
Details: VAPOR DIFFUSION METHOD, RESERVOIR SOLUTION 15% PEG8000 AND 0.2M AMMONIUM SULFATE. CRYOPROTECTANT 22.5% GLYCEROL, 15% PEG8000 AND 0.2M AMMONIUM SULFATE, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1
DetectorType: RIGAKU IMAGE PLATE RAXIS-V / Detector: IMAGE PLATE / Date: Apr 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 34147 / % possible obs: 94 % / Observed criterion σ(I): -1 / Redundancy: 4.45 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 29.35
Reflection shellResolution: 1.3→1.35 Å / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 17 / % possible all: 95

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1USM

1usm


Resolution: 1.3→19.25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2597898.79 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1689 5 %RANDOM
Rwork0.216 ---
obs0.216 34026 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.8819 Å2 / ksol: 0.37497 e/Å3
Displacement parametersBiso mean: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--0.82 Å20 Å2
3----1.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.3→19.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 15 223 1530
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.051.5
X-RAY DIFFRACTIONc_mcangle_it2.872
X-RAY DIFFRACTIONc_scbond_it3.942
X-RAY DIFFRACTIONc_scangle_it5.212.5
LS refinement shellResolution: 1.3→1.38 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 272 4.9 %
Rwork0.259 5301 -
obs--93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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