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- PDB-3kt7: Crystal structure of Tpa1 from Saccharomyces cerevisiae, a compon... -

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Basic information

Entry
Database: PDB / ID: 3kt7
TitleCrystal structure of Tpa1 from Saccharomyces cerevisiae, a component of the messenger ribonucleoprotein complex
ComponentsPKHD-type hydroxylase TPA1
KeywordsOXIDOREDUCTASE / Tpa1 / double-stranded beta helix fold / dioxygenase / iron / mRNP complex / prolyl hydroxylase
Function / homology
Function and homology information


peptidyl-proline di-hydroxylation / peptidyl-proline dioxygenase activity / regulation of translational termination / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / poly(A) binding / L-ascorbic acid binding / Protein hydroxylation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / regulation of translational fidelity / translational termination ...peptidyl-proline di-hydroxylation / peptidyl-proline dioxygenase activity / regulation of translational termination / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / poly(A) binding / L-ascorbic acid binding / Protein hydroxylation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / regulation of translational fidelity / translational termination / ferrous iron binding / nucleus / cytoplasm
Similarity search - Function
Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / TPA1/Ofd1, C-terminal / Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / Prolyl 3,4-dihydroxylase TPA1/OFD1, N-terminal domain / Oxoglutarate and iron-dependent oxygenase degradation C-term / 2OG-Fe(II) oxygenase superfamily / Double-stranded beta-helix / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain ...Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / TPA1/Ofd1, C-terminal / Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / Prolyl 3,4-dihydroxylase TPA1/OFD1, N-terminal domain / Oxoglutarate and iron-dependent oxygenase degradation C-term / 2OG-Fe(II) oxygenase superfamily / Double-stranded beta-helix / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / 4-Layer Sandwich / Jelly Rolls / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Prolyl 3,4-dihydroxylase TPA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsKim, H.S. / Kim, H.L. / Kim, K.H. / Kim, D.J. / Lee, S.J. / Yoon, J.Y. / Yoon, H.J. / Lee, H.Y. / Park, S.B. / Kim, S.-J. ...Kim, H.S. / Kim, H.L. / Kim, K.H. / Kim, D.J. / Lee, S.J. / Yoon, J.Y. / Yoon, H.J. / Lee, H.Y. / Park, S.B. / Kim, S.-J. / Lee, J.Y. / Suh, S.W.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Crystal structure of Tpa1 from Saccharomyces cerevisiae, a component of the messenger ribonucleoprotein complex
Authors: Kim, H.S. / Kim, H.L. / Kim, K.H. / Kim, D.J. / Lee, S.J. / Yoon, J.Y. / Yoon, H.J. / Lee, H.Y. / Park, S.B. / Kim, S.-J. / Lee, J.Y. / Suh, S.W.
History
DepositionNov 24, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PKHD-type hydroxylase TPA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6998
Polymers73,0211
Non-polymers6787
Water14,250791
1
A: PKHD-type hydroxylase TPA1
hetero molecules

A: PKHD-type hydroxylase TPA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,39816
Polymers146,0422
Non-polymers1,35714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4160 Å2
ΔGint-15 kcal/mol
Surface area46390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.293, 136.293, 79.832
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-703-

SO4

21A-807-

HOH

31A-1516-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PKHD-type hydroxylase TPA1 / Termination and polyadenylation protein 1


Mass: 73020.930 Da / Num. of mol.: 1 / Fragment: N-terminal truncated form (residues 21-644)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TPA1, YER049W / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta2(DE3)pLysS
References: UniProt: P40032, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor

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Non-polymers , 5 types, 798 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 791 / 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: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 200mM lithium sulfate, 100mM Tris-HCl, 25%(w/v) PEG 3350, 0.14mM ferrous ascorbate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.2399 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2399 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 82927 / % possible obs: 99.8 % / Redundancy: 20 % / Rmerge(I) obs: 0.061 / Χ2: 1.97 / Net I/σ(I): 17.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.77-1.818.20.41939461.15196.5
1.8-1.8319.20.35141421.188199.9
1.83-1.8719.30.30541041.2071100
1.87-1.9119.30.24141471.2751100
1.91-1.9519.30.19341331.334199.9
1.95-1.9919.40.1840991.412199.9
1.99-2.0419.40.15141141.5061100
2.04-2.119.40.12941561.6151100
2.1-2.1619.40.11741241.7371100
2.16-2.2319.50.10241221.8671100
2.23-2.3119.60.09341361.9721100
2.31-2.419.70.08741322.1411100
2.4-2.5119.90.08141532.2371100
2.51-2.6420.20.07541422.3561100
2.64-2.8120.60.06941782.4681100
2.81-3.0321.20.06141762.6251100
3.03-3.3321.80.05341732.7061100
3.33-3.8122.10.04641972.7511100
3.81-4.821.80.04142172.6581100
4.8-5020.90.03943362.534199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.849 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.205 4126 5 %RANDOM
Rwork0.179 ---
obs0.18 82438 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.56 Å2 / Biso mean: 24.621 Å2 / Biso min: 11.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.07 Å20 Å2
2---0.13 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.77→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4563 0 37 791 5391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224803
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.9656508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43724.744234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34215861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1141522
X-RAY DIFFRACTIONr_chiral_restr0.0760.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213659
X-RAY DIFFRACTIONr_mcbond_it0.5231.52851
X-RAY DIFFRACTIONr_mcangle_it1.02824635
X-RAY DIFFRACTIONr_scbond_it1.50631952
X-RAY DIFFRACTIONr_scangle_it2.5974.51872
LS refinement shellResolution: 1.771→1.817 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 301 -
Rwork0.264 5671 -
all-5972 -
obs--98.42 %

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