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- PDB-5w0x: Crystal structure of mouse TOR signaling pathway regulator-like (... -

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Basic information

Entry
Database: PDB / ID: 5w0x
TitleCrystal structure of mouse TOR signaling pathway regulator-like (TIPRL) delta 94-103
ComponentsTIP41-like protein
KeywordsSIGNALING PROTEIN / Butterfly-like fold Protein phosphotase 2A regulator
Function / homologyTIP41-like protein / TIP41-like family / : / protein phosphatase inhibitor activity / DNA damage checkpoint signaling / cytoplasm / TIP41-like protein
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.717 Å
AuthorsWu, C. / Zheng, A. / Li, J. / Satyshur, K. / Xing, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM096060-01 United States
CitationJournal: Nat Commun / Year: 2017
Title: Methylation-regulated decommissioning of multimeric PP2A complexes.
Authors: Wu, C.G. / Zheng, A. / Jiang, L. / Rowse, M. / Stanevich, V. / Chen, H. / Li, Y. / Satyshur, K.A. / Johnson, B. / Gu, T.J. / Liu, Z. / Xing, Y.
History
DepositionJun 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TIP41-like protein


Theoretical massNumber of molelcules
Total (without water)28,1911
Polymers28,1911
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.642, 63.642, 102.053
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein TIP41-like protein


Mass: 28190.967 Da / Num. of mol.: 1 / Fragment: UNP residues 12-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tiprl / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BH58
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Cacodylate pH6.5 15% PEG1000(v/v) 0.2M Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.717→48.495 Å / Num. obs: 12335 / % possible obs: 97.3 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.041 / Net I/σ(I): 31.94
Reflection shellResolution: 2.717→2.78 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.39 / Num. unique obs: 296 / Rpim(I) all: 0.266 / % possible all: 45.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2621: ???)refinement
APEXdata collection
HKL-2000712data processing
CRANK21.9.95phasing
RefinementMethod to determine structure: SAD / Resolution: 2.717→48.495 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 34.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2732 318 5.05 %10%
Rwork0.2076 ---
obs0.2111 12335 98.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.717→48.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 0 32 1773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011782
X-RAY DIFFRACTIONf_angle_d1.1852407
X-RAY DIFFRACTIONf_dihedral_angle_d4.51074
X-RAY DIFFRACTIONf_chiral_restr0.059268
X-RAY DIFFRACTIONf_plane_restr0.007305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7166-2.98990.41891520.3462804X-RAY DIFFRACTION95
2.9899-3.42250.31851600.26412953X-RAY DIFFRACTION100
3.4225-4.31160.28371580.19882970X-RAY DIFFRACTION100
4.3116-48.50280.23481530.17512985X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.26050.742-0.65635.20291.96467.93650.1626-0.1925-0.07240.519-0.37771.1178-0.4128-1.22450.07040.53090.05750.15470.89580.08410.93254.425622.4491-2.6757
23.9106-0.05720.2535.75821.60017.67840.3277-0.0161-0.38920.00710.1968-0.00490.3798-0.4338-0.44210.4838-0.0048-0.05980.60630.14770.627913.031116.0479-7.0032
35.36420.18110.91064.52992.80315.27420.0130.41520.4707-0.71980.02940.0703-0.9195-0.2432-0.01340.48610.09240.06210.48720.19240.561818.178929.8495-12.9021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 238 )

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