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

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Basic information

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


Phenylalanine metabolism / regulation of protein binding / 4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / L-phenylalanine metabolic process / phenylalanine 4-monooxygenase activity / tetrahydrobiopterin biosynthetic process / transcription coactivator activity / positive regulation of DNA-templated transcription / identical protein binding ...Phenylalanine metabolism / regulation of protein binding / 4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / L-phenylalanine metabolic process / phenylalanine 4-monooxygenase activity / 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
7,8-DIHYDROBIOPTERIN / 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: DCOH
B: DCOH
C: DCOH
D: DCOH
E: DCOH
F: DCOH
G: DCOH
H: DCOH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,05516
Polymers96,1418
Non-polymers1,9148
Water4,648258
1
A: DCOH
B: DCOH
C: DCOH
D: DCOH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0278
Polymers48,0704
Non-polymers9574
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-15 kcal/mol
Surface area17720 Å2
MethodPISA
2
E: DCOH
F: DCOH
G: DCOH
H: DCOH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0278
Polymers48,0704
Non-polymers9574
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.700, 105.700, 196.170
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: Chemical
ChemComp-HBI / 7,8-DIHYDROBIOPTERIN


Mass: 239.231 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H13N5O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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 / Detector: IMAGE PLATE / Date: Sep 29, 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: 46073 / % possible obs: 78.6 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.057
Reflection
*PLUS
Num. obs: 45971 / % possible obs: 78 % / Num. measured all: 312481
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.45 Å / % possible obs: 39 % / 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 / Num. reflection obs: 45971 / σ(F): 0 / Stereochemistry target values: TNT RESTRAINTS
Details: CORRELATED B-VALUE REFINEMENT WAS CARRIED OUT WITH TNT. MEAN B VALUE 14.8 ANGSTROMS**2 FINAL RMS COORD. SHIFT 0.01 ANGSTROMS
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6487 0 136 258 6881
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.008
X-RAY DIFFRACTIONt_gen_planes0.011
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.026
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.8 Å2
Refine LS restraints
*PLUS
Type: t_bond_d / Dev ideal: 0.011

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