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- PDB-4wil: Crystal structure of DCoH2 S51T -

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Basic information

Entry
Database: PDB / ID: 4wil
TitleCrystal structure of DCoH2 S51T
ComponentsPterin-4-alpha-carbinolamine dehydratase 2
KeywordsLYASE / bifunctional / kinetic stability / coactivator / tetrahydrobiopterin recycling
Function / homology
Function and homology information


4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / phenylalanine 4-monooxygenase activity / tetrahydrobiopterin biosynthetic process / positive regulation of DNA-templated transcription / mitochondrion / identical protein binding / nucleus
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 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsWang, D. / Rose, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-0643830 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Interactions with the Bifunctional Interface of the Transcriptional Coactivator DCoH1 Are Kinetically Regulated.
Authors: Wang, D. / Coco, M.W. / Rose, R.B.
History
DepositionSep 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pterin-4-alpha-carbinolamine dehydratase 2
B: Pterin-4-alpha-carbinolamine dehydratase 2


Theoretical massNumber of molelcules
Total (without water)23,8272
Polymers23,8272
Non-polymers00
Water3,855214
1
A: Pterin-4-alpha-carbinolamine dehydratase 2
B: Pterin-4-alpha-carbinolamine dehydratase 2

A: Pterin-4-alpha-carbinolamine dehydratase 2
B: Pterin-4-alpha-carbinolamine dehydratase 2


Theoretical massNumber of molelcules
Total (without water)47,6544
Polymers47,6544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5250 Å2
ΔGint-38 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.729, 57.729, 115.064
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-232-

HOH

21A-233-

HOH

31B-224-

HOH

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Components

#1: Protein Pterin-4-alpha-carbinolamine dehydratase 2 / PHS 2 / 4-alpha-hydroxy-tetrahydropterin dehydratase 2 / DcoH-like protein DCoHm / Dimerization ...PHS 2 / 4-alpha-hydroxy-tetrahydropterin dehydratase 2 / DcoH-like protein DCoHm / Dimerization cofactor of hepatocyte nuclear factor 1 from muscle / HNF-1-alpha dimerization cofactor


Mass: 11913.419 Da / Num. of mol.: 2 / Fragment: UNP residues 34-136 / Mutation: S51T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcbd2, Dcoh2, Dcohm / Plasmid: pET24b / Production host: Escherichia coli (E. coli)
References: UniProt: Q9CZL5, 4a-hydroxytetrahydrobiopterin dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.34 Å3/Da / Density % sol: 47.05 % / Description: hexagonal pyramids
Crystal growTemperature: 291 K / Method: evaporation / pH: 7.5
Details: 0.1M Tris, 8% PEG 8,000 mixing 0.5 ul protein and 1 ul reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 17, 2011 / Details: focussing mirror
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→25 Å / Num. obs: 48837 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 10.7 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.059 / Net I/σ(I): 58.1
Reflection shellResolution: 1.36→1.38 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.953 / Mean I/σ(I) obs: 2.98 / % possible all: 96.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.4_486) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RU0

1ru0


Resolution: 1.36→24.997 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.48 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1746 2291 5.08 %Random
Rwork0.1579 ---
obs0.1587 45081 92.34 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.1 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1-1.5014 Å2-0 Å2-0 Å2
2--1.5014 Å20 Å2
3----3.0027 Å2
Refinement stepCycle: LAST / Resolution: 1.36→24.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 0 0 214 1761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061591
X-RAY DIFFRACTIONf_angle_d1.0452153
X-RAY DIFFRACTIONf_dihedral_angle_d12.27553
X-RAY DIFFRACTIONf_chiral_restr0.078231
X-RAY DIFFRACTIONf_plane_restr0.005278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.357-1.38660.46041200.39092187X-RAY DIFFRACTION76
1.3866-1.41880.27931160.26942468X-RAY DIFFRACTION87
1.4188-1.45430.23051420.21282441X-RAY DIFFRACTION85
1.4543-1.49360.19591410.16972445X-RAY DIFFRACTION86
1.4936-1.53750.15911160.14882526X-RAY DIFFRACTION88
1.5375-1.58720.16681450.11272647X-RAY DIFFRACTION93
1.5872-1.64390.12431350.1022712X-RAY DIFFRACTION94
1.6439-1.70970.13611340.10432705X-RAY DIFFRACTION94
1.7097-1.78750.16221530.10992750X-RAY DIFFRACTION95
1.7875-1.88170.1441380.12482742X-RAY DIFFRACTION95
1.8817-1.99950.16091800.13762734X-RAY DIFFRACTION96
1.9995-2.15380.15621520.14212797X-RAY DIFFRACTION97
2.1538-2.37040.16851530.14042837X-RAY DIFFRACTION98
2.3704-2.71310.16971400.16772904X-RAY DIFFRACTION99
2.7131-3.41680.17291680.16862956X-RAY DIFFRACTION99
3.4168-25.00160.18721580.17592939X-RAY DIFFRACTION95

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