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

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Basic information

Entry
Database: PDB / ID: 1rjd
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 / S-ADENOSYLMETHIONINE / Leucine carboxyl methyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 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 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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)117,46213
Polymers115,7023
Non-polymers1,76010
Water13,781765
1
A: carboxy methyl transferase for protein phosphatase 2A catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1224
Polymers38,5671
Non-polymers5553
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)39,1224
Polymers38,5671
Non-polymers5553
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)39,2185
Polymers38,5671
Non-polymers6514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.683, 110.683, 165.879
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-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 765 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.48 %
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: BM30A / Wavelength: 0.94, 0.9792, 0.9795, 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 14, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.941
20.97921
30.97951
40.91841
ReflectionResolution: 1.8→52 Å / Num. obs: 106254 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.9 Å / % possible all: 100
Reflection
*PLUS
Lowest resolution: 52 Å / % possible obs: 100 % / Redundancy: 5.9 % / Num. measured all: 631127 / Rmerge(I) obs: 0.13

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→52.7 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.498 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21515 5424 5.1 %RANDOM
Rwork0.17777 ---
obs0.17968 100754 100 %-
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: 13.683 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→52.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7998 0 110 765 8873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0218272
X-RAY DIFFRACTIONr_bond_other_d0.0020.027563
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.97511183
X-RAY DIFFRACTIONr_angle_other_deg0.804317650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6165988
X-RAY DIFFRACTIONr_chiral_restr0.0840.21255
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028928
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021623
X-RAY DIFFRACTIONr_nbd_refined0.2480.21825
X-RAY DIFFRACTIONr_nbd_other0.240.28865
X-RAY DIFFRACTIONr_nbtor_other0.0830.24728
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2636
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.370.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.233
X-RAY DIFFRACTIONr_mcbond_it0.7711.54961
X-RAY DIFFRACTIONr_mcangle_it1.41228028
X-RAY DIFFRACTIONr_scbond_it2.19733311
X-RAY DIFFRACTIONr_scangle_it3.5594.53136
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 410
Rwork0.23 7452
Refinement
*PLUS
Lowest resolution: 52 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.214 / Rfactor Rwork: 0.172
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_deg0.78

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