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- PDB-1dch: CRYSTAL STRUCTURE OF DCOH, A BIFUNCTIONAL, PROTEIN-BINDING TRANSC... -

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Basic information

Entry
Database: PDB / ID: 1dch
TitleCRYSTAL STRUCTURE OF DCOH, A BIFUNCTIONAL, PROTEIN-BINDING TRANSCRIPTION COACTIVATOR
ComponentsDCOH (DIMERIZATION COFACTOR OF HNF-1)
KeywordsTRANSCRIPTIONAL STIMULATOR / DIMERIZATION / TRANSCRIPTIONAL SIMULATOR / 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
Pterin-4-alpha-carbinolamine dehydratase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsEndrizzi, J.A. / Cronk, J.D. / Wang, W. / Crabtree, G.R. / Alber, T.
CitationJournal: 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
DepositionJan 24, 1995Processing site: BNL
Revision 1.0Mar 8, 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

Downloads & links

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Assembly

Deposited unit
A: DCOH (DIMERIZATION COFACTOR OF HNF-1)
B: DCOH (DIMERIZATION COFACTOR OF HNF-1)
C: DCOH (DIMERIZATION COFACTOR OF HNF-1)
D: DCOH (DIMERIZATION COFACTOR OF HNF-1)
E: DCOH (DIMERIZATION COFACTOR OF HNF-1)
F: DCOH (DIMERIZATION COFACTOR OF HNF-1)
G: DCOH (DIMERIZATION COFACTOR OF HNF-1)
H: DCOH (DIMERIZATION COFACTOR OF HNF-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,90916
Polymers96,1418
Non-polymers7698
Water00
1
A: DCOH (DIMERIZATION COFACTOR OF HNF-1)
B: DCOH (DIMERIZATION COFACTOR OF HNF-1)
C: DCOH (DIMERIZATION COFACTOR OF HNF-1)
D: DCOH (DIMERIZATION COFACTOR OF HNF-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4558
Polymers48,0704
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-93 kcal/mol
Surface area17860 Å2
MethodPISA
2
E: DCOH (DIMERIZATION COFACTOR OF HNF-1)
F: DCOH (DIMERIZATION COFACTOR OF HNF-1)
G: DCOH (DIMERIZATION COFACTOR OF HNF-1)
H: DCOH (DIMERIZATION COFACTOR OF HNF-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4558
Polymers48,0704
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-93 kcal/mol
Surface area17690 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
Atom site foot note1: MET A 103 - THR A 104 OMEGA = 143.40 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein
DCOH (DIMERIZATION COFACTOR OF HNF-1) / PHS / PHENYLALANINE HYDROXYLASE STIMULATOR PROTEIN / 4A-CARBINOLAMINE DEHYDRATASE / PCD


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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4

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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: 62.59 %
Crystal growpH: 7.2
Details: pH 7.2 COMPND ROOM TEMP., 1.7M AMSO4, .1M HEPES, PH 7.2.
Crystal
*PLUS
Density % sol: 65 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein11
25 mM12KPO4
35 mMmethionine12
41.2 Mammonium sulfate12
52 %PEG40012
60.1 MHEPES12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.54
DetectorDate: May 26, 1994
RadiationMonochromator: RAXIS II C / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 4 % / Rmerge(I) obs: 0.06
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. obs: 21436 / % possible obs: 82.2 % / Num. measured all: 86670 / Rmerge(I) obs: 0.06

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 3→6 Å / σ(F): 0 /
RfactorNum. reflection
obs0.184 18054
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6495 0 40 0 6535
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg2.9
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.019
X-RAY DIFFRACTIONt_gen_planes0.031
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.042
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 12 Å2

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