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- PDB-3ily: Apo crystal structure of protein tyrosine phosphatase from Entamo... -

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Basic information

Entry
Database: PDB / ID: 3ily
TitleApo crystal structure of protein tyrosine phosphatase from Entamoeba histolytica featuring a disordered active site
ComponentsProtein tyrosine phosphatase, putative
KeywordsHYDROLASE / NIAID / SSGCID / Seattle Structural Genomics Center for Infectious Disease / parasitic protozoan / dysentery
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / protein tyrosine phosphatase activity
Similarity search - Function
: / Protein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2014
Title: Crystal structure and putative substrate identification for the Entamoeba histolytica low molecular weight tyrosine phosphatase.
Authors: Linford, A.S. / Jiang, N.M. / Edwards, T.E. / Sherman, N.E. / Van Voorhis, W.C. / Stewart, L.J. / Myler, P.J. / Staker, B.L. / Petri, W.A.
History
DepositionAug 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Apr 9, 2014Group: Database references
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Revision 1.5Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein tyrosine phosphatase, putative
B: Protein tyrosine phosphatase, putative


Theoretical massNumber of molelcules
Total (without water)40,7652
Polymers40,7652
Non-polymers00
Water1,26170
1
A: Protein tyrosine phosphatase, putative


Theoretical massNumber of molelcules
Total (without water)20,3821
Polymers20,3821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein tyrosine phosphatase, putative


Theoretical massNumber of molelcules
Total (without water)20,3821
Polymers20,3821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.674, 45.674, 132.329
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Protein tyrosine phosphatase, putative


Mass: 20382.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS (eukaryote)
Gene: EHI_153650 / Production host: Escherichia coli (E. coli) / References: UniProt: C4LSE7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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

Crystal growMethod: vapor diffusion, sitting drop
Details: ProPlex Screen condition A9, 0.1 M MES pH 6.0, 20% PEG MME 2000, 0.2 M NaCl, 20% glycerol as cryo-protectant, 26.1 mg/mL protein, crystal tracking ID 203694a9, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→22.84 Å / Num. obs: 13504 / % possible obs: 98.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.063 / Χ2: 1.042 / Net I/σ(I): 23.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1154 / Χ2: 0.957 / % possible all: 85.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.5 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å23.11 Å
Translation3 Å23.11 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB enry 3IDO

3ido


Resolution: 2.2→22.84 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.207 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.77 / SU B: 7.815 / SU ML: 0.198 / SU R Cruickshank DPI: 0.379 / SU Rfree: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.379 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.264 670 5 %RANDOM
Rwork0.209 ---
obs0.211 13465 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.12 Å2 / Biso mean: 37.906 Å2 / Biso min: 21.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2--0.94 Å20 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 2.2→22.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 0 70 2287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222278
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9673069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3815279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8624.545110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.01715405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7451513
X-RAY DIFFRACTIONr_chiral_restr0.1110.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211715
X-RAY DIFFRACTIONr_mcbond_it0.9151.51408
X-RAY DIFFRACTIONr_mcangle_it1.67222265
X-RAY DIFFRACTIONr_scbond_it2.3563870
X-RAY DIFFRACTIONr_scangle_it3.8294.5802
LS refinement shellResolution: 2.203→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 35 -
Rwork0.245 822 -
all-857 -
obs--84.43 %

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