[English] 日本語
Yorodumi
- PDB-3rgo: Crystal Structure of PTPMT1 -

+
Open data


ID or keywords:

Loading...

-
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 tyrosine/serine/threonine phosphatase activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / myosin phosphatase activity / protein-serine/threonine phosphatase ...phosphatidylglycerophosphatase / phosphatidylglycerophosphatase activity / cardiolipin biosynthetic process / regulation of intrinsic apoptotic signaling pathway / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol metabolic process / protein tyrosine/serine/threonine phosphatase activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / myosin phosphatase activity / protein-serine/threonine phosphatase / dephosphorylation / 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 / Dual specificity protein phosphatase domain profile. / 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 / Dual specificity protein phosphatase domain profile. / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: MAD

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more