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- PDB-5bx1: Crystal Structure of PRL-1 complex with compound analogy 3 -

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Basic information

Entry
Database: PDB / ID: 5bx1
TitleCrystal Structure of PRL-1 complex with compound analogy 3
ComponentsProtein tyrosine phosphatase type IVA 1
KeywordsHYDROLASE / monomer / protein tyrosine phosphatase / interface / detrimerizer
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
Chem-4XA / Protein tyrosine phosphatase type IVA 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLiu, S. / Bai, Y. / Zhang, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal Structure of PRL-1 complex with compound analogy 3
Authors: Liu, S. / Bai, Y. / Zhang, Z.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein tyrosine phosphatase type IVA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5624
Polymers18,0121
Non-polymers5503
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein tyrosine phosphatase type IVA 1
hetero molecules

A: Protein tyrosine phosphatase type IVA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1238
Polymers36,0242
Non-polymers1,0996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2060 Å2
ΔGint-73 kcal/mol
Surface area14200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.070, 76.471, 86.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein tyrosine phosphatase type IVA 1 / PTP(CAAXI) / Protein-tyrosine phosphatase 4a1 / Protein-tyrosine phosphatase of regenerating liver 1 / PRL-1


Mass: 18012.029 Da / Num. of mol.: 1 / Fragment: UNP residues 4-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTP4A1, PRL1, PTPCAAX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93096, protein-tyrosine-phosphatase
#2: Chemical ChemComp-4XA / 3-(5,6-dimethyl-2H-isoindol-2-yl)-N'-[(E)-furan-2-ylmethylidene]benzohydrazide


Mass: 357.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19N3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop
Details: 1.9 M amino sulfate, 100 mM sodium acetate, pH 4.6 ~ 4.9
PH range: pH 4.6 ~ 4.9

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 03/22/2012
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. all: 14049 / Num. obs: 13768 / % possible obs: 98 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.113 / Rsym value: 0.07 / Net I/av σ(I): 14.1 / Net I/σ(I): 14.1
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 0.66 / % possible all: 69.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZCK

1zck


Resolution: 1.9→50 Å / Data cutoff high absF: 17600 / Data cutoff low absF: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.24 460 3.6 %Random selection
Rwork0.195 ---
obs-11901 87.2 %-
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 37 100 1367
LS refinement shellResolution: 1.9→1.98 Å /
RfactorNum. reflection
Rfree0.307 35
Rwork0.285 853

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