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- PDB-3s4o: Protein Tyrosine Phosphatase (putative) from Leishmania major -

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Basic information

Entry
Database: PDB / ID: 3s4o
TitleProtein Tyrosine Phosphatase (putative) from Leishmania major
ComponentsProtein tyrosine phosphatase-like protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
Function / homology
Function and homology information


kinetoplast / protein tyrosine/serine/threonine phosphatase activity / phosphatase activity / : / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / host cell cytoplasm / extracellular exosome / nucleus ...kinetoplast / protein tyrosine/serine/threonine phosphatase activity / phosphatase activity / : / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / host cell cytoplasm / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase / 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 profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase / 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
THIOSULFATE / Protein tyrosine phosphatase PRL-1
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsMerritt, E.A. / Arakaki, T. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP) / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Protein Tyrosine Phosphatase from Leishmania major
Authors: Merritt, E.A. / Arakaki, T. / Neely, H. / Phizicky, E. / Quartley, E. / Van Voorhis, W.C. / Buckner, F.S. / Fan, E. / Zucker, F. / Verlinde, C.L.M.J. / Hol, W.G.J.
History
DepositionMay 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein tyrosine phosphatase-like protein
B: Protein tyrosine phosphatase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3734
Polymers37,0222
Non-polymers3502
Water1,58588
1
A: Protein tyrosine phosphatase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8623
Polymers18,5111
Non-polymers3502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein tyrosine phosphatase-like protein


Theoretical massNumber of molelcules
Total (without water)18,5111
Polymers18,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.518, 69.420, 118.931
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-like protein


Mass: 18511.084 Da / Num. of mol.: 2 / Fragment: sequence database residues 4-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: LmjF16.0230, LMJF_16_0230 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QEZ7, protein-tyrosine-phosphatase
#2: Chemical ChemComp-THJ / THIOSULFATE / Thiosulfate


Mass: 112.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O3S2
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: protein buffer 25 mM HEPES pH 7.5, 500 mM NaCl, crystallization buffer 100 mM Sodium thiosulfate pentahydrate, 100 mM HEPES pH 7.0, 35% PEG 4000, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97955, 0.97967, 0.95369
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979551
20.979671
30.953691
ReflectionResolution: 2.16→50 Å / Num. obs: 17137 / % possible obs: 87.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.112 / Χ2: 0.993 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.16-2.242.80.239340.732148.3
2.24-2.333.50.21112620.883166.5
2.33-2.434.20.21614990.949178.4
2.43-2.565.10.19517060.969188.3
2.56-2.726.30.16818380.976195.6
2.72-2.9370.13719170.994199
2.93-3.237.10.09519370.968199.1
3.23-3.696.90.07819521.054199.5
3.69-4.656.80.09619831.073199.4
4.65-506.30.12821090.995199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
SHELX+ phaserphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→45.16 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.2578 / WRfactor Rwork: 0.2145 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8192 / SU B: 15.73 / SU ML: 0.187 / SU R Cruickshank DPI: 0.4087 / SU Rfree: 0.2539 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.409 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: RIDING HYDROGEN ATOMS
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 777 5.1 %RANDOM
Rwork0.2065 ---
obs0.2086 15341 94.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.75 Å2 / Biso mean: 47.6157 Å2 / Biso min: 23.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 20 88 2656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222649
X-RAY DIFFRACTIONr_bond_other_d0.0040.021826
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.9473593
X-RAY DIFFRACTIONr_angle_other_deg1.1893.0014464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2445330
X-RAY DIFFRACTIONr_chiral_restr0.0680.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022769
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02503
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 43 -
Rwork0.27 729 -
all-772 -
obs--69.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
123.39883.2601-10.7439.6606-3.369815.7948-0.00281.19071.2971-0.858-0.0916-0.2517-1.179-0.15570.09440.72370.0015-0.05660.23080.11780.235123.026-0.421-20.436
22.3349-0.3820.96582.5-0.25133.9564-0.02960.00890.0650.02880.06180.18270.0871-0.2281-0.03210.327-0.0180.00840.1110.02340.048818.66-13.563-14.829
36.5934-0.8898-1.695512.9379-2.02068.2075-0.3658-0.16430.2860.63140.39450.1029-0.84850.4381-0.02880.5125-0.0531-0.03450.1608-0.02480.096927.076-2.732-4.294
48.5953-6.22570.733133.260313.57727.2162-0.0697-0.95160.95731.54350.3831-1.3495-0.81210.3976-0.31340.5437-0.0004-0.03230.4040.03840.194317.3162.034-32.559
53.0724-0.81180.79013.8764-1.30035.860.14590.1717-0.2346-0.42710.07110.37780.4766-0.4424-0.2170.4249-0.0568-0.07570.24440.08950.13535.979-8.172-36.539
63.76721.203-1.79877.9655-1.88668.3616-0.10470.0639-0.0862-0.13580.25490.32530.044-0.2651-0.15030.42650.06810.00380.16390.07470.047612.6214.1-46.138
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 16
2X-RAY DIFFRACTION2A17 - 133
3X-RAY DIFFRACTION3A134 - 163
4X-RAY DIFFRACTION4B1 - 16
5X-RAY DIFFRACTION5B17 - 118
6X-RAY DIFFRACTION6B119 - 163

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