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- PDB-2yn2: Huf protein - paralogue of the tau55 histidine phosphatase domain -

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Basic information

Entry
Database: PDB / ID: 2yn2
TitleHuf protein - paralogue of the tau55 histidine phosphatase domain
ComponentsUNCHARACTERIZED PROTEIN YNL108C
KeywordsHYDROLASE / HISTIDINE PHOSPHATASE DOMAIN / PHOSPHOGLYCERATE MUTASE DOMAIN
Function / homology
Function and homology information


phosphatase activity / dephosphorylation / nucleus / cytoplasm
Similarity search - Function
Transcription factor TFIIIC subunit Tfc7/tau55 / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Uncharacterized protein YNL108C
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsTaylor, N.M.I. / Glatt, S. / Hennrich, M. / von Scheven, G. / Grotsch, H. / Fernandez-Tornero, C. / Rybin, V. / Gavin, A.C. / Kolb, P. / Muller, C.W.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural and Functional Characterization of a Phosphatase Domain within Yeast General Transcription Factor Tfiiic.
Authors: Taylor, N.M.I. / Glatt, S. / Hennrich, M.L. / Von Scheven, G. / Grotsch, H. / Fernandez-Tornero, C. / Rybin, V. / Gavin, A. / Kolb, P. / Muller, C.W.
History
DepositionOct 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Structure summary
Revision 1.3Jun 12, 2013Group: Database references
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: UNCHARACTERIZED PROTEIN YNL108C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0192
Polymers31,9731
Non-polymers461
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.720, 86.720, 98.960
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 UNCHARACTERIZED PROTEIN YNL108C / HUF7P


Mass: 31973.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI BL21 (bacteria) / Variant (production host): PRARE / References: UniProt: P53929
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.36 Å3/Da / Density % sol: 63.46 % / Description: NONE
Crystal growpH: 5.9 / Details: 0.2 M MAGNESIUM FORMATE, 26% PEG 3,350, pH 5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97633
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97633 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 27487 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 11.17 % / Biso Wilson estimate: 44.322 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.19
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 11.38 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2.54 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YN0 (EDITED WITH SCULPTOR)
Resolution: 2.05→43.36 Å / SU ML: 0.29 / σ(F): 1.81 / Phase error: 28.56 / Stereochemistry target values: ML
Details: RESIDUES 2-263 ARE VISIBLE IN THE ELECTRON DENSITY, EXCEPT FOR RESIDUES 209-216, WHICH ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2363 1376 5 %
Rwork0.1998 --
obs0.2017 27399 99.63 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.055 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 62.54 Å2
Baniso -1Baniso -2Baniso -3
1-9.6647 Å20 Å20 Å2
2--9.6647 Å20 Å2
3----19.3293 Å2
Refinement stepCycle: LAST / Resolution: 2.05→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 3 110 2156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072106
X-RAY DIFFRACTIONf_angle_d0.9132855
X-RAY DIFFRACTIONf_dihedral_angle_d13.467792
X-RAY DIFFRACTIONf_chiral_restr0.054298
X-RAY DIFFRACTIONf_plane_restr0.005372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0499-2.12320.34941460.30582554X-RAY DIFFRACTION99
2.1232-2.20820.331320.28382527X-RAY DIFFRACTION99
2.2082-2.30870.31231300.25972583X-RAY DIFFRACTION100
2.3087-2.43040.29961320.242564X-RAY DIFFRACTION99
2.4304-2.58270.26421330.23392585X-RAY DIFFRACTION100
2.5827-2.7820.26141360.22232598X-RAY DIFFRACTION100
2.782-3.06190.25441500.22312593X-RAY DIFFRACTION100
3.0619-3.50480.26281380.21442601X-RAY DIFFRACTION100
3.5048-4.4150.20181460.17222647X-RAY DIFFRACTION100
4.415-43.36970.1991330.17132771X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.61330.28680.7560.23320.28241.0704-0.01270.26880.02310.1017-0.07060.0852-0.21990.295200.4206-0.0757-0.01890.3920.0140.3998-8.913147.3973-4.0034
20.0967-0.00440.04320.03190.01250.0232-0.74150.1754-0.04670.2776-0.06730.8561-0.3216-0.0964-0.00010.72390.06620.24270.53120.04020.6086-19.841854.516512.782
30.87930.1944-0.24610.272-0.28610.25220.02880.04830.02370.13520.0210.01250.07140.29300.4039-0.0635-0.00920.36990.02290.3583-6.081343.9855.5365
40.252-0.0995-0.22880.1809-0.01590.2222-0.0254-0.026-0.11710.13360.1823-0.24720.28890.6313-00.56270.0931-0.07240.6552-0.03960.4821.169933.8816-2.9083
50.06040.0649-0.0070.0393-0.02990.0035-0.0587-0.3627-0.52130.09550.5303-0.0462-0.7051-0.08050.00010.405-0.1234-0.06140.7177-0.00450.52863.611846.85157.8186
60.34480.0182-0.1590.6754-0.26710.15250.2298-0.0298-0.16480.4876-0.0421-0.11460.62330.24980.00010.6258-0.0577-0.05710.41960.03440.4628-9.312829.11327.6434
70.01070.00660.0133-0.00560.02210.0563-0.41380.1807-0.79040.8859-0.36970.57840.31160.06970.00020.8034-0.10840.05190.5179-0.01750.4578-10.049340.966423.0993
80.09980.09770.12210.069-0.03470.10230.1266-0.06960.07490.27710.10250.02880.2733-0.1146-0.00010.4269-0.1058-0.0060.36810.00430.4006-17.739135.06354.7884
90.05370.04240.06480.0834-0.00590.08240.24650.2585-0.2969-0.1135-0.26390.19330.3597-0.2986-0.00010.6265-0.145-0.00510.6624-0.03630.6911-30.601931.7066-1.0868
100.6432-0.17470.15480.2183-0.02710.08880.1286-0.1350.21210.2197-0.15550.1101-0.1425-0.092300.3934-0.04620.02780.4513-0.04630.4168-22.42240.49743.4476
110.04890.0295-0.04980.0011-0.00930.046-0.5806-0.47190.2156-0.18750.5999-0.13030.4178-0.0581-0.00020.6814-0.18760.12590.63120.0590.5043-22.744931.944816.4169
120.04670.39090.29620.6353-0.00890.6452-0.00150.18070.0060.10260.153-0.12560.2093-0.19220.00010.3595-0.0134-0.04480.4489-0.02240.4352-18.789441.7584-6.6113
130.0394-0.01670.0641-0.01220.00450.046-0.5096-0.32690.4967-0.5317-0.72190.07090.43140.073-0.00190.5444-0.1088-0.09330.55850.01060.5484-16.230841.8154-20.1703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:52)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 53:57)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 58:94)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 95:111)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 112:121)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 122:154)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 155:161)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 162:185)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 186:192)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 193:217)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 218:224)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 225:255)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 256:263)

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