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

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Basic information

Entry
Database: PDB / ID: 1usm
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: 1.2 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 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
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

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Assembly

Deposited unit
A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)9,5091
Polymers9,5091
Non-polymers00
Water2,648147
1
A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA

A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)19,0172
Polymers19,0172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.625, 55.625, 125.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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


Mass: 9508.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DIMERIZATION DOMAIN / Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P83819*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.15 Å3/Da / Density % sol: 42.4 %
Crystal growMethod: microbatch / pH: 5.3
Details: MICROBATCH METHOD UNDER OIL BY CRYSTALLIZATION ROBOT TERA. 25.6 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH 3.15M SODIUM FORMATE AND 0.1M SODIUM ACETATE BUFFER, PH 4.0. FINAL PH WAS 5.3. ...Details: MICROBATCH METHOD UNDER OIL BY CRYSTALLIZATION ROBOT TERA. 25.6 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH 3.15M SODIUM FORMATE AND 0.1M SODIUM ACETATE BUFFER, PH 4.0. FINAL PH WAS 5.3. CRYOPROTECTANT CONTENT WAS: 25% GLYCEROL, 2.0M SODIUM FORMATE, AND 0.6M SODIUM ACETATE BUFFER, PH 4.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8
DetectorType: RIGAKU IMAGE PLATE RAXIS-V / Detector: IMAGE PLATE / Date: Feb 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 30991 / % possible obs: 98.7 % / Observed criterion σ(I): -0.2 / Redundancy: 8.7 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 41.4
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 11.7 / % possible all: 99.5

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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 1DCO

1dco


Resolution: 1.2→18.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3515920.09 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 7-9 ARE DISORDERED AND NOT INCLUDED IN THE MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1539 5 %RANDOM
Rwork0.215 ---
obs0.215 30967 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.4998 Å2 / ksol: 0.393311 e/Å3
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2---0.86 Å20 Å2
3---1.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.2→18.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms646 0 0 147 793
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_deg1.1
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_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.811.5
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scbond_it3.652
X-RAY DIFFRACTIONc_scangle_it5.032.5
LS refinement shellResolution: 1.2→1.28 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 251 4.9 %
Rwork0.246 4839 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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