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

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Basic information

Entry
Database: PDB / ID: 1rjg
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 / regulation of autophagy / protein-containing complex assembly / methylation
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
S-ADENOSYL-L-HOMOCYSTEINE / Leucine carboxyl methyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsLeulliot, N. / Quevillon-Cheruel, S. / Sorel, I. / Li de La Sierra-Gallay, I. / 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. / Li de La Sierra-Gallay, I. / 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: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,9522
Polymers38,5671
Non-polymers3841
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.837, 74.098, 85.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein carboxy methyl transferase for protein phosphatase 2A catalytic subunit / ppm1p


Mass: 38567.438 Da / Num. of mol.: 1
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 1.92 Å3/Da / Density % sol: 35.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% PEG 4000, 0.2M magnesium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13 mg/mlprotein1drop
224 %PEG40001reservoir
30.2 M1reservoirMgCl2
40.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 25, 2002
RadiationMonochromator: 1.5418 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→56.8 Å / Num. obs: 21568 / % possible obs: 83.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.87→1.97 Å / % possible all: 85.2
Reflection
*PLUS
Redundancy: 3.3 % / Num. measured all: 71628 / Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD ENTRY 1RJD

1rjd


Resolution: 2.61→37.01 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.847 / SU B: 12.439 / SU ML: 0.271 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28928 452 4.8 %RANDOM
Rwork0.181 ---
obs0.18624 8997 99.75 %-
all-8997 --
Displacement parametersBiso mean: 40.435 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.61→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 26 20 2401
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.084
LS refinement shellResolution: 2.61→2.678 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 18
Rwork0.192 626
Refinement
*PLUS
Highest resolution: 1.87 Å / Lowest resolution: 56.8 Å / Num. reflection obs: 20438 / Num. reflection Rfree: 1109 / % reflection Rfree: 5 % / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 0.84

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