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- PDB-3c5v: PP2A-specific methylesterase apo form (PME) -

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Basic information

Entry
Database: PDB / ID: 3c5v
TitlePP2A-specific methylesterase apo form (PME)
ComponentsProtein phosphatase methylesterase 1
KeywordsHYDROLASE / demethylase / PP2A / Alternative splicing / Phosphoprotein / Serine esterase
Function / homology
Function and homology information


protein phosphatase methylesterase-1 / : / protein phosphatase inhibitor activity / lncRNA binding / Cyclin A/B1/B2 associated events during G2/M transition / protein phosphatase 2A binding / G2/M transition of mitotic cell cycle / protein phosphatase binding / cadherin binding / protein kinase binding / nucleoplasm
Similarity search - Function
Protein phosphatase methylesterase, eukaryotic / Lipases, serine active site. / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein phosphatase methylesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsXing, Y. / Li, Z. / Chen, Y. / Stock, J. / Jeffrey, P.D. / Shi, Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structural mechanism of demethylation and inactivation of protein phosphatase 2A.
Authors: Xing, Y. / Li, Z. / Chen, Y. / Stock, J.B. / Jeffrey, P.D. / Shi, Y.
History
DepositionFeb 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein phosphatase methylesterase 1


Theoretical massNumber of molelcules
Total (without water)34,7441
Polymers34,7441
Non-polymers00
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.512, 82.512, 90.843
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein phosphatase methylesterase 1 / PME-1


Mass: 34743.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPME1, PME1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y570
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPME-1 WITH INTERNAL PROTEOLYTIC DELETION (DELTA 249-280)

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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: 52.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 26% v/v Jeffamine-2001, 200mM sodium chloride, 5mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
SYNCHROTRONNSLS X2520.97945, 0.97910, 0.96410
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 10, 2005
ADSC QUANTUM 3152CCDMar 18, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.979451
30.97911
40.96411
ReflectionResolution: 2→100 Å / Num. all: 25077 / Num. obs: 25077 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 16.8 Å2 / Rsym value: 0.074
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.293 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→19.9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1749029.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1191 4.8 %RANDOM
Rwork0.183 ---
all0.183 24574 --
obs0.183 24574 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.3381 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å20 Å20 Å2
2---1.43 Å20 Å2
3---2.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 0 283 2561
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.162.5
X-RAY DIFFRACTIONc_mcangle_it3.013
X-RAY DIFFRACTIONc_scbond_it3.53
X-RAY DIFFRACTIONc_scangle_it4.883.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 196 4.9 %
Rwork0.211 3821 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

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