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- PDB-3rgq: Crystal Structure of PTPMT1 in complex with PI(5)P -

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Basic information

Entry
Database: PDB / ID: 3rgq
TitleCrystal Structure of PTPMT1 in complex with PI(5)P
ComponentsProtein-tyrosine phosphatase mitochondrial 1
KeywordsHYDROLASE / phosphatidylglycerol phosphate (PGP) phosphatase
Function / homology
Function and homology information


phosphatidylglycerophosphatase / phosphatidylglycerophosphatase activity / cardiolipin biosynthetic process / regulation of intrinsic apoptotic signaling pathway / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol metabolic process / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity ...phosphatidylglycerophosphatase / phosphatidylglycerophosphatase activity / cardiolipin biosynthetic process / regulation of intrinsic apoptotic signaling pathway / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol metabolic process / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / mitochondrial inner membrane / mitochondrion
Similarity search - Function
Phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1 / Phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1-like / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. ...Phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1 / Phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1-like / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-5P5 / Phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsXiao, J. / Engel, J.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural and functional analysis of PTPMT1, a phosphatase required for cardiolipin synthesis.
Authors: Xiao, J. / Engel, J.L. / Zhang, J. / Chen, M.J. / Manning, G. / Dixon, J.E.
History
DepositionApr 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Aug 3, 2011Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Feb 21, 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

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Assembly

Deposited unit
A: Protein-tyrosine phosphatase mitochondrial 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3372
Polymers17,7831
Non-polymers5541
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.019, 67.914, 32.088
Angle α, β, γ (deg.)90.000, 96.560, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-273-

HOH

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Components

#1: Protein Protein-tyrosine phosphatase mitochondrial 1 / PTEN-like phosphatase / Phosphoinositide lipid phosphatase


Mass: 17782.557 Da / Num. of mol.: 1 / Mutation: C200S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plip, Ptpmt1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q66GT5, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical ChemComp-5P5 / (2R)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,4,6-tetrahydroxy-5-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dibutanoate


Mass: 554.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H32O16P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3350, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 11902 / % possible obs: 97.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.062 / Χ2: 0.639 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.093.40.245640.588192.6
2.09-2.123.50.225570.565192.7
2.12-2.163.50.1875700.574195.5
2.16-2.213.70.1755760.527197
2.21-2.263.70.1626090.568197.6
2.26-2.313.70.155870.596197.5
2.31-2.373.80.1255940.578198.7
2.37-2.433.80.1256010.638198.4
2.43-2.53.80.1075920.533198
2.5-2.583.80.0965920.573198.7
2.58-2.683.70.0876170.593198.1
2.68-2.783.80.0825730.621199.3
2.78-2.913.80.0716120.645198.2
2.91-3.063.70.0685830.745199.3
3.06-3.253.70.0556230.753198.7
3.25-3.513.70.055960.798199.2
3.51-3.863.60.0455970.823199.3
3.86-4.423.60.0396140.793199.4
4.42-5.563.70.0366160.657199.2
5.56-503.60.0316290.594199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.59 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.72 Å
Translation2.5 Å44.72 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.6.3_473refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→44.715 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8657 / SU ML: 0.22 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2146 572 4.81 %
Rwork0.1729 --
obs0.1748 11896 97.48 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.157 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso max: 97.19 Å2 / Biso mean: 27.9437 Å2 / Biso min: 9.21 Å2
Baniso -1Baniso -2Baniso -3
1-11.9438 Å20 Å2-2.6031 Å2
2---5.9825 Å20 Å2
3----5.9613 Å2
Refinement stepCycle: LAST / Resolution: 2.05→44.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 31 141 1420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031303
X-RAY DIFFRACTIONf_angle_d0.7721765
X-RAY DIFFRACTIONf_chiral_restr0.059204
X-RAY DIFFRACTIONf_plane_restr0.003216
X-RAY DIFFRACTIONf_dihedral_angle_d21.115523
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.25150.24781450.18192704284994
2.2515-2.57730.23631370.17522840297798
2.5773-3.2470.23721440.17512871301599
3.247-44.72550.18451460.16842909305599
Refinement TLS params.Method: refined / Origin x: 28.2624 Å / Origin y: -7.0844 Å / Origin z: 7.1619 Å
111213212223313233
T0.1151 Å2-0.0111 Å20.0097 Å2-0.0862 Å2-0.0018 Å2--0.072 Å2
L1.3066 °20.6601 °20.9097 °2-1.3861 °20.6783 °2--1.751 °2
S0.1067 Å °-0.1279 Å °-0.0273 Å °0.2326 Å °-0.1079 Å °-0.003 Å °0.2234 Å °-0.002 Å °-0.0005 Å °
Refinement TLS groupSelection details: ALL

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