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- PDB-5c16: Myotubularin-related proetin 1 -

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Basic information

Entry
Database: PDB / ID: 5c16
TitleMyotubularin-related proetin 1
ComponentsMyotubularin-related protein 1
KeywordsHYDROLASE / MTMR / phosphatase
Function / homology
Function and homology information


phosphatidylinositol-3,5-bisphosphate 3-phosphatase / phosphatidylinositol-3-phosphatase / regulation of phosphatidylinositol dephosphorylation / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / phosphatidylinositol-3-phosphate phosphatase activity / phosphatidylinositol dephosphorylation / phosphatidylinositol biosynthetic process / Synthesis of PIPs at the plasma membrane / protein tyrosine phosphatase activity / protein homodimerization activity ...phosphatidylinositol-3,5-bisphosphate 3-phosphatase / phosphatidylinositol-3-phosphatase / regulation of phosphatidylinositol dephosphorylation / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / phosphatidylinositol-3-phosphate phosphatase activity / phosphatidylinositol dephosphorylation / phosphatidylinositol biosynthetic process / Synthesis of PIPs at the plasma membrane / protein tyrosine phosphatase activity / protein homodimerization activity / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Myotubularin-related protein 1 / MTMR1, PH-GRAM / Myotubularin-like, phosphatase domain / Myotubularin family / Myotubularin-like phosphatase domain / Myotubularin phosphatase domain. / domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins / GRAM domain / GRAM domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) ...Myotubularin-related protein 1 / MTMR1, PH-GRAM / Myotubularin-like, phosphatase domain / Myotubularin family / Myotubularin-like phosphatase domain / Myotubularin phosphatase domain. / domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins / GRAM domain / GRAM domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / 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 / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Myotubularin-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.07 Å
AuthorsLee, B.I. / Bong, S.M.
CitationJournal: Plos One / Year: 2016
Title: Crystal Structure of Human Myotubularin-Related Protein 1 Provides Insight into the Structural Basis of Substrate Specificity
Authors: Bong, S.M. / Son, K.B. / Yang, S.W. / Park, J.W. / Cho, J.W. / Kim, K.T. / Kim, H. / Kim, S.J. / Kim, Y.J. / Lee, B.I.
History
DepositionJun 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myotubularin-related protein 1
B: Myotubularin-related protein 1
C: Myotubularin-related protein 1
D: Myotubularin-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,18310
Polymers261,6134
Non-polymers5706
Water11,746652
1
A: Myotubularin-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5933
Polymers65,4031
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myotubularin-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5933
Polymers65,4031
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Myotubularin-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4982
Polymers65,4031
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Myotubularin-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4982
Polymers65,4031
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.219, 96.587, 97.581
Angle α, β, γ (deg.)87.60, 86.07, 77.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Myotubularin-related protein 1 / Phosphatidylinositol-3-phosphate phosphatase


Mass: 65403.289 Da / Num. of mol.: 4 / Fragment: UNP residues 95-665 / Mutation: C438S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTMR1 / Plasmid: modified pET32 vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: Q13613, phosphatidylinositol-3-phosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Sodium-HEPES, PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 136495 / % possible obs: 86.1 % / Redundancy: 2.5 % / Net I/σ(I): 18.9
Reflection shellResolution: 2.07→2.11 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 3.2 / % possible all: 84

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
HKL-2000data scaling
HKL-2000data processing
RefinementResolution: 2.07→34.814 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 2.35 / Phase error: 39.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2735 6200 4.97 %
Rwork0.2203 --
obs0.2229 124830 85.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→34.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15824 0 30 652 16506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816260
X-RAY DIFFRACTIONf_angle_d1.0422048
X-RAY DIFFRACTIONf_dihedral_angle_d13.695880
X-RAY DIFFRACTIONf_chiral_restr0.0412396
X-RAY DIFFRACTIONf_plane_restr0.0052792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.09350.42382060.36673866X-RAY DIFFRACTION84
2.0935-2.11820.37782090.36883863X-RAY DIFFRACTION84
2.1182-2.1440.37522140.36023868X-RAY DIFFRACTION84
2.144-2.17110.41612330.33663904X-RAY DIFFRACTION85
2.1711-2.19970.3891990.32943865X-RAY DIFFRACTION84
2.1997-2.22980.33962240.31493887X-RAY DIFFRACTION84
2.2298-2.26170.35882230.31373872X-RAY DIFFRACTION85
2.2617-2.29540.35511780.29853911X-RAY DIFFRACTION84
2.2954-2.33130.3412320.29283892X-RAY DIFFRACTION85
2.3313-2.36950.33982120.27513885X-RAY DIFFRACTION85
2.3695-2.41030.30432120.25683992X-RAY DIFFRACTION86
2.4103-2.45410.27061750.25093986X-RAY DIFFRACTION86
2.4541-2.50130.31952050.25173960X-RAY DIFFRACTION85
2.5013-2.55240.31082110.24783922X-RAY DIFFRACTION86
2.5524-2.60790.33481840.2374011X-RAY DIFFRACTION87
2.6079-2.66850.2792020.23474003X-RAY DIFFRACTION87
2.6685-2.73520.28682360.21813942X-RAY DIFFRACTION86
2.7352-2.80910.26681980.21724013X-RAY DIFFRACTION87
2.8091-2.89180.30432180.21823968X-RAY DIFFRACTION87
2.8918-2.9850.27822120.2094057X-RAY DIFFRACTION87
2.985-3.09170.29191720.20964053X-RAY DIFFRACTION88
3.0917-3.21540.26712070.21314097X-RAY DIFFRACTION88
3.2154-3.36160.2731900.19594022X-RAY DIFFRACTION87
3.3616-3.53870.25951880.1854038X-RAY DIFFRACTION87
3.5387-3.76010.21842050.1734094X-RAY DIFFRACTION89
3.7601-4.05010.22751990.16194051X-RAY DIFFRACTION88
4.0501-4.45690.19582300.15753975X-RAY DIFFRACTION86
4.4569-5.10010.19222130.15663896X-RAY DIFFRACTION85
5.1001-6.4190.25522160.18554069X-RAY DIFFRACTION88
6.419-34.81890.20561970.19123668X-RAY DIFFRACTION80
Refinement TLS params.Method: refined / Origin x: 1.0033 Å / Origin y: 23.8041 Å / Origin z: -21.9029 Å
111213212223313233
T-0.2275 Å20.0012 Å2-0.0892 Å2--0.0086 Å20.0053 Å2--0.0139 Å2
L0.1674 °20.0275 °20.061 °2--0.0574 °20.0476 °2--0.3476 °2
S0.0455 Å °-0.0173 Å °0.0181 Å °-0.1635 Å °0.0592 Å °-0.0805 Å °-0.4899 Å °-0.1326 Å °0.095 Å °
Refinement TLS groupSelection details: all

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