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

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Basic information

Entry
Database: PDB / ID: 1rje
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 / C-terminal protein methylation / regulation of autophagy / protein-containing complex assembly / cytosol
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 / S-ADENOSYL-L-HOMOCYSTEINE / Leucine carboxyl methyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: 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)117,51614
Polymers115,7023
Non-polymers1,81411
Water17,835990
1
A: carboxy methyl transferase for protein phosphatase 2A catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2045
Polymers38,5671
Non-polymers6374
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)39,2045
Polymers38,5671
Non-polymers6374
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)39,1084
Polymers38,5671
Non-polymers5413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.747, 110.747, 165.613
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 990 / 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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 8000, 0.2M ammonium sulfate, 0.1M MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13 mg/mlprotein1drop
215 %PEG80001reservoir
30.1 Mpotassium phosphate1reservoiror sodium phosphate, pH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2002
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→24 Å / Num. obs: 76511 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.11 Å / % possible all: 92
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 24 Å / Redundancy: 3.8 % / Num. measured all: 294159 / Rmerge(I) obs: 0.12

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24.47 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.885 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.163 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21031 3851 5 %RANDOM
Rwork0.15878 ---
obs0.16138 72598 98.74 %-
all-72598 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.526 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2→24.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7998 0 112 990 9100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0218273
X-RAY DIFFRACTIONr_bond_other_d0.0020.027554
X-RAY DIFFRACTIONr_angle_refined_deg0.791.97511183
X-RAY DIFFRACTIONr_angle_other_deg0.857317632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3695988
X-RAY DIFFRACTIONr_chiral_restr0.0460.21255
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028928
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021623
X-RAY DIFFRACTIONr_nbd_refined0.2550.21909
X-RAY DIFFRACTIONr_nbd_other0.2450.28876
X-RAY DIFFRACTIONr_nbtor_other0.0850.24736
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2805
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3420.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.245
X-RAY DIFFRACTIONr_mcbond_it0.8431.54961
X-RAY DIFFRACTIONr_mcangle_it1.57728028
X-RAY DIFFRACTIONr_scbond_it2.51633312
X-RAY DIFFRACTIONr_scangle_it4.1284.53136
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.268 224
Rwork0.223 4794
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 24 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.005
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg0.79

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