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- PDB-3hxa: Crystal Structure of DCoH1Thr51Ser -

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Basic information

Entry
Database: PDB / ID: 3hxa
TitleCrystal Structure of DCoH1Thr51Ser
ComponentsPterin-4-alpha-carbinolamine dehydratase
KeywordsLYASE / alpha and beta structure / Nucleus / Tetrahydrobiopterin biosynthesis
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsRho, H.Y. / Jones, C.N. / Rose, R.B.
Citation
Journal: To be Published
Title: Crystal Structure of DCoH1Thr51Ser
Authors: Rho, H.Y. / Jones, C.N. / Rose, R.B.
#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.
#2: Journal: Biochemistry / Year: 2004
Title: Biochemical and structural basis for partially redundant enzymatic and transcriptional functions of DCoH and DCoH2
Authors: Rose, R.B. / Pullen, K.E. / Bayle, J.H. / Crabtree, G.R. / Alber, T.
History
DepositionJun 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pterin-4-alpha-carbinolamine dehydratase
B: Pterin-4-alpha-carbinolamine dehydratase
C: Pterin-4-alpha-carbinolamine dehydratase
D: Pterin-4-alpha-carbinolamine dehydratase
E: Pterin-4-alpha-carbinolamine dehydratase
F: Pterin-4-alpha-carbinolamine dehydratase
G: Pterin-4-alpha-carbinolamine dehydratase
H: Pterin-4-alpha-carbinolamine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,53424
Polymers96,0298
Non-polymers1,50516
Water9,440524
1
A: Pterin-4-alpha-carbinolamine dehydratase
B: Pterin-4-alpha-carbinolamine dehydratase
C: Pterin-4-alpha-carbinolamine dehydratase
D: Pterin-4-alpha-carbinolamine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,67511
Polymers48,0144
Non-polymers6617
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-100 kcal/mol
Surface area17430 Å2
MethodPISA
2
E: Pterin-4-alpha-carbinolamine dehydratase
F: Pterin-4-alpha-carbinolamine dehydratase
G: Pterin-4-alpha-carbinolamine dehydratase
H: Pterin-4-alpha-carbinolamine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,85913
Polymers48,0144
Non-polymers8459
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-104 kcal/mol
Surface area17390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.805, 103.805, 193.629
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Pterin-4-alpha-carbinolamine dehydratase / PHS / 4-alpha-hydroxy-tetrahydropterin dehydratase / Phenylalanine hydroxylase-stimulating protein ...PHS / 4-alpha-hydroxy-tetrahydropterin dehydratase / Phenylalanine hydroxylase-stimulating protein / Pterin carbinolamine dehydratase / PCD / Dimerization cofactor of hepatocyte nuclear factor 1-alpha / Dimerization cofactor of HNF1 / DCoH


Mass: 12003.576 Da / Num. of mol.: 8 / Mutation: T51S
Source method: isolated from a genetically manipulated source
Details: GST-FUSION / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dcoh, Pcbd, PCBD/DCoH, Pcbd1 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P61459, 4a-hydroxytetrahydrobiopterin dehydratase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O

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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: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 7.5
Details: HEPES, Ammonium Sulfate, PEG 200, Glycerol, pH 7.5, Hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→81.54 Å / Num. obs: 111375 / % possible obs: 99.1 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 2.958
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.98.20.9210.8129054156950.92196.6
1.9-2.019.70.571.2146377151410.5798.7
2.01-2.159.70.3282.1138188143150.32899
2.15-2.329.70.2192.9129545134190.21999.6
2.32-2.559.80.1693.7121502124330.16999.8
2.55-2.85100.1254.3112804113100.125100
2.85-3.2910.30.1054.810259099930.105100
3.29-4.0210.60.0995.19030985230.099100
4.02-5.6910.80.0835.57255766880.083100
5.69-81.5410.40.0864.34022338580.086100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.1.9data scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.226 5521 4.9 %
Rwork0.211 --
obs-111045 98.8 %
Solvent computationBsol: 57.222 Å2
Displacement parametersBiso max: 73.94 Å2 / Biso mean: 32.07 Å2 / Biso min: 11.65 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å2-0.342 Å20 Å2
2---2.29 Å20 Å2
3---4.581 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6305 0 88 524 6917
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.198
X-RAY DIFFRACTIONc_mcbond_it1.2261.5
X-RAY DIFFRACTIONc_scbond_it1.8762
X-RAY DIFFRACTIONc_mcangle_it1.9122
X-RAY DIFFRACTIONc_scangle_it2.8082.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5gol.paramgol.top

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