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- PDB-1rjf: Structure of PPM1, a leucine carboxy methyltransferase involved i... -

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Basic information

Entry
Database: PDB / ID: 1rjf
TitleStructure of PPM1, a leucine carboxy methyltransferase involved in the regulation of protein phosphatase 2A activity
Componentscarboxy methyl transferase for protein phosphatase 2A catalytic subunit
KeywordsTRANSFERASE / SAM dependent methyltransferase
Function / homology
Function and homology information


Cyclin A/B1/B2 associated events during G2/M transition / [phosphatase 2A protein]-leucine-carboxy methyltransferase / protein C-terminal leucine carboxyl O-methyltransferase activity / protein-containing complex assembly / methylation / regulation of autophagy
Similarity search - Function
Leucine carboxyl methyltransferase 1 / Methyltransferase Ppm1/Ppm2/Tcmp / Leucine carboxyl methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Leucine carboxyl methyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLeulliot, N. / Quevillon-Cheruel, S. / Sorel, I. / de La Sierra-Gallay, I.L. / Collinet, B. / Graille, M. / Blondeau, K. / Bettache, N. / Poupon, A. / Janin, J. / van Tilbeurgh, H.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure of protein phosphatase methyltransferase 1 (PPM1), a leucine carboxyl methyltransferase involved in the regulation of protein phosphatase 2A activity
Authors: Leulliot, N. / Quevillon-Cheruel, S. / Sorel, I. / de La Sierra-Gallay, I.L. / Collinet, B. / Graille, M. / Blondeau, K. / Bettache, N. / Poupon, A. / Janin, J. / van Tilbeurgh, H.
History
DepositionNov 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: carboxy methyl transferase for protein phosphatase 2A catalytic subunit
B: carboxy methyl transferase for protein phosphatase 2A catalytic subunit
C: carboxy methyl transferase for protein phosphatase 2A catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,35511
Polymers115,7023
Non-polymers6538
Water4,900272
1
A: carboxy methyl transferase for protein phosphatase 2A catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9085
Polymers38,5671
Non-polymers3404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: carboxy methyl transferase for protein phosphatase 2A catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7243
Polymers38,5671
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: carboxy methyl transferase for protein phosphatase 2A catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7243
Polymers38,5671
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.395, 112.395, 162.848
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein carboxy methyl transferase for protein phosphatase 2A catalytic subunit / PPM1p


Mass: 38567.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PPM1 / Plasmid: pET9 / Production host: Escherichia coli (E. coli) / Strain (production host): Xl-10 Gold
References: UniProt: Q04081, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 15% PEG 8000, 0.1M K/NaPO4, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 3 mg/ml / Common name: protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 14, 2002
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 53908 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.25→2.37 Å / % possible all: 86
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 5.4 % / Num. measured all: 290033 / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.895 / SU B: 5.657 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.28 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23899 2738 5.1 %RANDOM
Rwork0.1829 ---
obs0.1857 51135 97.63 %-
all-51135 --
Displacement parametersBiso mean: 31.998 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.35 Å20 Å2
2--0.71 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7836 0 36 272 8144
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d0.8
LS refinement shellResolution: 2.25→2.307 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.28 145
Rwork0.229 2849
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS

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