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- PDB-1xm2: Crystal structure of Human PRL-1 -

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Basic information

Entry
Database: PDB / ID: 1xm2
TitleCrystal structure of Human PRL-1
ComponentsTyrosine PhosphataseProtein tyrosine phosphatase
KeywordsHYDROLASE
Function / homology
Function and homology information


protein tyrosine/serine/threonine phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / spindle / early endosome / positive regulation of cell migration / cell cycle / endoplasmic reticulum ...protein tyrosine/serine/threonine phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / spindle / early endosome / positive regulation of cell migration / cell cycle / endoplasmic reticulum / nucleus / cytoplasm
Similarity search - Function
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 / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. ...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 / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Protein tyrosine phosphatase type IVA 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsJeong, D.G. / Kim, S.J. / Kim, J.H. / Son, J.H. / Ryu, S.E.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Trimeric structure of PRL-1 phosphatase reveals an active enzyme conformation and regulation mechanisms
Authors: Jeong, D.G. / Kim, S.J. / Kim, J.H. / Son, J.H. / Park, M.R. / Lim, S.M. / Yoon, T.S. / Ryu, S.E.
History
DepositionOct 1, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine Phosphatase
B: Tyrosine Phosphatase
C: Tyrosine Phosphatase
D: Tyrosine Phosphatase
E: Tyrosine Phosphatase
F: Tyrosine Phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,95812
Polymers120,3816
Non-polymers5766
Water1,65792
1
A: Tyrosine Phosphatase
B: Tyrosine Phosphatase
C: Tyrosine Phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4796
Polymers60,1913
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Tyrosine Phosphatase
E: Tyrosine Phosphatase
F: Tyrosine Phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4796
Polymers60,1913
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.290, 84.760, 122.180
Angle α, β, γ (deg.)90.00, 99.79, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a trimer. Two trimers exist in the asymmetric unit.

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Components

#1: Protein
Tyrosine Phosphatase / Protein tyrosine phosphatase / PRL-1


Mass: 20063.527 Da / Num. of mol.: 6 / Mutation: C104S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q93096, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4K, Sodium Acetate, AMS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.979, 0.9792, 0.9794, 0.9716
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: May 16, 2003 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97921
30.97941
40.97161
ReflectionResolution: 2.7→40 Å / Num. all: 32950 / Num. obs: 31124 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 7.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4531 / Rsym value: 0.26 / % possible all: 95.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1546 -random
Rwork0.237 ---
all0.243 32950 --
obs0.237 31124 94.5 %-
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7080 0 30 92 7202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_dihedral_angle_d23.17
X-RAY DIFFRACTIONo_improper_angle_d0.93

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