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

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Basic information

Entry
Database: PDB / ID: 1dco
TitleDCOH, A BIFUNCTIONAL PROTEIN-BINDING TRANSCRIPTIONAL COACTIVATOR
ComponentsDCOH
KeywordsTRANSCRIPTIONAL STIMULATOR / DIMERIZATION COFACTOR / DEHYDRATASE / 4A-CARBINOLAMINE DEHYDRATASE / TRANSREGULATOR OF HOMEODOMAIN PROTEINS
Function / homology
Function and homology information


Phenylalanine metabolism / 4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / L-phenylalanine metabolic process / phenylalanine 4-monooxygenase activity / regulation of protein binding / tetrahydrobiopterin biosynthetic process / transcription coactivator activity / positive regulation of DNA-templated transcription / identical protein binding ...Phenylalanine metabolism / 4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / L-phenylalanine metabolic process / phenylalanine 4-monooxygenase activity / regulation of protein binding / tetrahydrobiopterin biosynthetic process / transcription coactivator activity / positive regulation of DNA-templated transcription / identical protein binding / nucleus / cytoplasm
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
Pterin-4-alpha-carbinolamine dehydratase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsCronk, J.D. / Endrizzi, J.A. / Alber, T.
Citation
Journal: Protein Sci. / Year: 1996
Title: High-resolution structures of the bifunctional enzyme and transcriptional coactivator DCoH and its complex with a product analogue.
Authors: Cronk, J.D. / Endrizzi, J.A. / Alber, T.
#1: Journal: Science / Year: 1995
Title: Crystal Structure of DCoH, a Bifunctional, Protein-Binding Transcriptional Coactivator
Authors: Endrizzi, J.A. / Cronk, J.D. / Wang, W. / Crabtree, G.R. / Alber, T.
History
DepositionMay 16, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DCOH
B: DCOH
C: DCOH
D: DCOH
E: DCOH
F: DCOH
G: DCOH
H: DCOH


Theoretical massNumber of molelcules
Total (without water)96,1418
Polymers96,1418
Non-polymers00
Water4,089227
1
A: DCOH
B: DCOH
C: DCOH
D: DCOH


Theoretical massNumber of molelcules
Total (without water)48,0704
Polymers48,0704
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-34 kcal/mol
Surface area17820 Å2
MethodPISA
2
E: DCOH
F: DCOH
G: DCOH
H: DCOH


Theoretical massNumber of molelcules
Total (without water)48,0704
Polymers48,0704
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-35 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.650, 105.650, 196.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
DCOH / DIMERIZATION COFACTOR OF HEPATOCYTE NUCLEAR FACTOR 1-ALPHA / HNF-1 / PHS / PHENYLALANINE ...DIMERIZATION COFACTOR OF HEPATOCYTE NUCLEAR FACTOR 1-ALPHA / HNF-1 / PHS / PHENYLALANINE HYDROXYLASE STIMULATOR


Mass: 12017.603 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Description: GST-FUSION / Organ: LIVER / Plasmid: PGEX-2T (PHARMACIA) / Production host: Escherichia coli (E. coli)
References: UniProt: P61459, 4a-hydroxytetrahydrobiopterin dehydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 65 %
Crystal growpH: 7.4 / Details: ROOM TEMPERATURE, 1.7M AMSO4, 0.1M HEPES, PH 7.4 / Temp details: room temp

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 20, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 44232 / % possible obs: 75.6 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.072
Reflection
*PLUS
Num. obs: 43794 / % possible obs: 75 % / Num. measured all: 310522
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.45 Å / % possible obs: 33 % / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
TNTrefinement
R-AXISdata reduction
R-AXISdata scaling
RefinementResolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: TNT RESTRAINTS
Details: CORRELATED B-VALUE REFINEMENT WAS CARRIED OUT WITH TNT. MEAN B VALUE 14.7 ANGSTROMS**2 FINAL RMS COORD. SHIFT 0.01 ANGSTROMS
Num. reflection% reflection
obs43794 75.6 %
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6482 0 0 227 6709
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d15
X-RAY DIFFRACTIONt_angle_deg2.7
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.01
X-RAY DIFFRACTIONt_gen_planes0.014
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.052
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.4

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