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- PDB-3ido: Crystal structure of protein tyrosine phosphatase from Entamoeba ... -

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Basic information

Entry
Database: PDB / ID: 3ido
TitleCrystal structure of protein tyrosine phosphatase from Entamoeba histolytica with a phosphotyrosine crude mimic HEPES molecule in the active site
ComponentsProtein tyrosine phosphatase
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 / SYNCHROTRON / 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
DepositionJul 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 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 1.5Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.6Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Protein tyrosine phosphatase
B: Protein tyrosine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2414
Polymers40,7652
Non-polymers4772
Water2,360131
1
A: Protein tyrosine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6212
Polymers20,3821
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein tyrosine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6212
Polymers20,3821
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.579, 70.409, 79.189
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein tyrosine phosphatase /


Mass: 20382.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Expressed with an N-terminal his tag and 3C protease cleavage site. Expression tag not removed prior to crystallization. Construct contains an Ala at residue 85 not a Val as indicated by ...Details: Expressed with an N-terminal his tag and 3C protease cleavage site. Expression tag not removed prior to crystallization. Construct contains an Ala at residue 85 not a Val as indicated by genomics project. Residue 85 is in the interior of the protein and does not appear to accommodate a Val. Switching from a Val to Ala is GYN.
Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS (eukaryote)
Gene: EHI_153650 / Production host: Escherichia coli (E. coli) / References: UniProt: C4LSE7
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: ProPlex condition F1, 0.1 M Hepes pH 7.0, 20% PEG 8000, 25% glycerol as cryo-protectant, 26.1 mg/mL protein, 0.1 mg/mL chymotrypsin, crystal tracking ID 203694f1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.2→45.93 Å / Num. obs: 17494 / % possible obs: 98.6 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.14 / Χ2: 0.993 / Net I/σ(I): 7.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.43 / Num. unique all: 1539 / Χ2: 0.942 / % possible all: 89.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.57 Å48.12 Å
Translation2.57 Å48.12 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1xww

1xww


Resolution: 2.2→45.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.259 / WRfactor Rwork: 0.206 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.803 / SU B: 6.675 / SU ML: 0.166 / SU R Cruickshank DPI: 0.312 / SU Rfree: 0.231 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.312 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.254 887 5.1 %RANDOM
Rwork0.204 ---
obs0.206 17445 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.75 Å2 / Biso mean: 36.713 Å2 / Biso min: 21.85 Å2
Baniso -1Baniso -2Baniso -3
1--2.71 Å20 Å20 Å2
2---0.15 Å20 Å2
3---2.87 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 30 131 2685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222602
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.9753502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.645314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.57824.516124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64215472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8391514
X-RAY DIFFRACTIONr_chiral_restr0.0840.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211944
X-RAY DIFFRACTIONr_mcbond_it0.5761.51572
X-RAY DIFFRACTIONr_mcangle_it1.09522540
X-RAY DIFFRACTIONr_scbond_it1.54131030
X-RAY DIFFRACTIONr_scangle_it2.5424.5962
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 66 -
Rwork0.281 1061 -
all-1127 -
obs--87.03 %

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