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- PDB-3mgu: Structure of S. cerevisiae Tpa1 protein, a proline hydroxylase mo... -

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Basic information

Entry
Database: PDB / ID: 3mgu
TitleStructure of S. cerevisiae Tpa1 protein, a proline hydroxylase modifying ribosomal protein Rps23
ComponentsPKHD-type hydroxylase TPA1
KeywordsOXIDOREDUCTASE / translation termination / prolyl-4-hydroxylase / dioxygenase / DSBH
Function / homology
Function and homology information


peptidyl-proline di-hydroxylation / peptidyl-proline dioxygenase activity / 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 / regulation of translational termination / 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 / 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 / regulation of translational termination / 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
: / Prolyl 3,4-dihydroxylase TPA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsHenri, J. / Rispal, D. / Bayart, E. / van Tilbeurgh, H. / Seraphin, B. / Graille, M.
CitationJournal: To be Published
Title: Structural and functional insights into S. cerevisiae Tpa1, a putative prolyl hydroxylase influencing translation termination and transcription
Authors: Henri, J. / Rispal, D. / Bayart, E. / van Tilbeurgh, H. / Seraphin, B. / Graille, M.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 3, 2018Group: Structure summary / Category: struct / Item: _struct.title

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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)74,1972
Polymers74,1411
Non-polymers561
Water59433
1
A: PKHD-type hydroxylase TPA1
hetero molecules

A: PKHD-type hydroxylase TPA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3944
Polymers148,2832
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4000 Å2
ΔGint-10 kcal/mol
Surface area43740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.180, 104.840, 205.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 74141.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TPA1, YER049W / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 pLysS Novagen
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
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes pH7.5, 44% methylpentanediol, 0.1M Mg(NO3)2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9796, 0.9794, 0.9843
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97941
30.98431
ReflectionResolution: 2.8→46.7 Å / Num. all: 23000 / Num. obs: 22109 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.58 % / Biso Wilson estimate: 52.1 Å2 / Net I/σ(I): 6.76
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.64 % / % possible all: 92.5

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Processing

Software
NameVersionClassification
MXCUBEdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→19.92 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.693 / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 2.07 / Phase error: 35.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2964 1106 5 %random
Rwork0.2394 ---
all0.25 22109 --
obs0.2424 22109 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.315 Å2 / ksol: 0.295 e/Å3
Displacement parametersBiso max: 127.06 Å2 / Biso mean: 67.173 Å2 / Biso min: 34.81 Å2
Baniso -1Baniso -2Baniso -3
1--22.943 Å20 Å2-0 Å2
2--51.417 Å20 Å2
3----28.474 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 1 33 4406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064481
X-RAY DIFFRACTIONf_angle_d1.0776048
X-RAY DIFFRACTIONf_dihedral_angle_d19.7371658
X-RAY DIFFRACTIONf_chiral_restr0.075646
X-RAY DIFFRACTIONf_plane_restr0.004772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7893-2.91620.38791350.36022564X-RAY DIFFRACTION98
2.9162-3.06990.45161350.33582567X-RAY DIFFRACTION99
3.0699-3.26220.37111370.30272607X-RAY DIFFRACTION99
3.2622-3.5140.35831370.25122603X-RAY DIFFRACTION99
3.514-3.86750.29751380.21492619X-RAY DIFFRACTION99
3.8675-4.42680.2351380.18752628X-RAY DIFFRACTION99
4.4268-5.57580.23651400.19022655X-RAY DIFFRACTION100
5.5758-46.70420.25941460.23422760X-RAY DIFFRACTION99

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