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- PDB-3rgo: Crystal Structure of PTPMT1 -

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Basic information

Entry
Database: PDB / ID: 3rgo
TitleCrystal Structure of PTPMT1
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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.928 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 / Item: _software.classification / _software.name
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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)18,1193
Polymers17,9271
Non-polymers1922
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.453, 36.453, 230.024
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 17926.816 Da / Num. of mol.: 1
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 5000 MME, Bis-Tris, (NH4)2SO4, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.111
SYNCHROTRONALS 8.2.120.9798, 0.9800, 0.9573
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDDec 19, 2009
ADSC QUANTUM 315r2CCDJan 29, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97981
30.981
40.95731
ReflectionRedundancy: 7.4 % / Av σ(I) over netI: 61.88 / Number: 86345 / Rmerge(I) obs: 0.063 / Χ2: 1.83 / D res high: 2 Å / D res low: 50 Å / Num. obs: 11679 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.435098.610.0517.3356.1
4.315.4399.810.054.8926.9
3.764.3199.810.0493.9197.1
3.423.7610010.0553.4717.1
3.173.4210010.0623.0987.3
2.993.1710010.0622.1287.4
2.842.9910010.0661.5517.5
2.712.8410010.0741.3767.4
2.612.7110010.0871.1887.6
2.522.6110010.0980.987.6
2.442.5210010.1150.9027.6
2.372.4410010.1390.8177.7
2.312.3710010.1470.7677.6
2.252.3110010.1820.7367.6
2.22.2510010.1860.6517.8
2.152.210010.2430.6517.6
2.112.1510010.2840.5997.7
2.072.1110010.330.5957.8
2.032.0710010.4010.5827.7
22.0310010.5210.5627
ReflectionResolution: 1.928→50 Å / Num. obs: 12762 / % possible obs: 99.9 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.051 / Χ2: 1.224 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.928-1.9613.20.7055960.5091,2100
1.96-213.20.5786270.5411,2100
2-2.0413.30.4466200.5961,2100
2.04-2.0813.30.3695880.6631,2100
2.08-2.1213.40.2976270.7211,2100
2.12-2.1713.10.2556280.7561,2100
2.17-2.2313.40.2086010.8281,2100
2.23-2.2913.20.1946360.9081,2100
2.29-2.3613.10.1546240.9791,2100
2.36-2.4313.30.1366281.0251,2100
2.43-2.5213.10.1136061.0791,2100
2.52-2.6212.90.0976621.1671,2100
2.62-2.74130.086141.3181,2100
2.74-2.8812.60.0726381.5031,2100
2.88-3.0612.60.0646461.7521,299.5
3.06-3.312.20.0586442.1021,2100
3.3-3.6311.90.0556532.5821,299.8
3.63-4.1611.10.0456592.4281,299.7
4.16-5.2411.40.0377002.0151,299.9
5.24-5010.80.0287651.31,298.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.928→34.749 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8212 / SU ML: 0.25 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 618 4.88 %
Rwork0.2271 --
obs0.2279 12667 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.546 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 186.99 Å2 / Biso mean: 51.7747 Å2 / Biso min: 30.38 Å2
Baniso -1Baniso -2Baniso -3
1-2.7305 Å20 Å2-0 Å2
2--2.7305 Å20 Å2
3----5.461 Å2
Refinement stepCycle: LAST / Resolution: 1.928→34.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1257 0 10 48 1315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041289
X-RAY DIFFRACTIONf_angle_d0.7761743
X-RAY DIFFRACTIONf_chiral_restr0.055198
X-RAY DIFFRACTIONf_plane_restr0.003217
X-RAY DIFFRACTIONf_dihedral_angle_d16.639473
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 (%)
1.928-2.12160.31081570.24992879303699
2.1216-2.42860.2831550.230429573112100
2.4286-3.05940.27031460.224530073153100
3.0594-34.7550.21961600.223132063366100
Refinement TLS params.Method: refined / Origin x: 13.1083 Å / Origin y: -1.3176 Å / Origin z: -15.3095 Å
111213212223313233
T0.3722 Å20.0068 Å20.1559 Å2-0.1683 Å2-0.0307 Å2--0.3159 Å2
L2.1035 °2-0.0219 °20.1938 °2-2.0857 °20.5842 °2--4.5529 °2
S0.0463 Å °-0.0883 Å °0.0804 Å °0.0657 Å °-0.0658 Å °-0.1551 Å °0.0337 Å °0.1107 Å °-0.0069 Å °
Refinement TLS groupSelection details: ALL

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