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- PDB-1d1q: CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSIN... -

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Basic information

Entry
Database: PDB / ID: 1d1q
TitleCRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE (LTP1) COMPLEXED WITH THE SUBSTRATE PNPP
ComponentsTYROSINE PHOSPHATASE (E.C.3.1.3.48)
KeywordsHYDROLASE / BETA-ALPHA-BETA
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein dephosphorylation / nucleus / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, low molecular weight / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-NITROPHENYL PHOSPHATE / PHOSPHATE ION / Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsWang, S. / Tabernero, L. / Zhang, M. / Harms, E. / Van Etten, R.L. / Staufacher, C.V.
Citation
Journal: Biochemistry / Year: 2000
Title: Crystal structures of a low-molecular weight protein tyrosine phosphatase from Saccharomyces cerevisiae and its complex with the substrate p-nitrophenyl phosphate.
Authors: Wang, S. / Tabernero, L. / Zhang, M. / Harms, E. / Van Etten, R.L. / Stauffacher, C.V.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Cloning and Characterization of a Saccharomyces cerevisiae Gene Encoding the Low Molecular Weight Protein-tyrosine Phosphatase
Authors: Ostanin, K. / Pokalsky, C. / Wang, S. / Van Etten, R.L.
History
DepositionSep 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYROSINE PHOSPHATASE (E.C.3.1.3.48)
B: TYROSINE PHOSPHATASE (E.C.3.1.3.48)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7485
Polymers37,3422
Non-polymers4063
Water6,630368
1
A: TYROSINE PHOSPHATASE (E.C.3.1.3.48)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8902
Polymers18,6711
Non-polymers2191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TYROSINE PHOSPHATASE (E.C.3.1.3.48)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8583
Polymers18,6711
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)45.897, 64.151, 112.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TYROSINE PHOSPHATASE (E.C.3.1.3.48)


Mass: 18671.154 Da / Num. of mol.: 2 / Mutation: C13A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Plasmid: PET23A / Production host: Escherichia coli (E. coli) / References: UniProt: P40347, protein-tyrosine-phosphatase
#2: Chemical ChemComp-4NP / 4-NITROPHENYL PHOSPHATE / Para-Nitrophenylphosphate


Mass: 219.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6NO6P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
Compound detailsInactive mutant of LTP1 that the nucleophile cysteine is mutated to alanine.

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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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 3400, Bis-TRIS, sodium chloride para-nitrophenyl phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 32773 / Num. obs: 32773 / % possible obs: 87.8 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 24.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.242 / Num. unique all: 1835 / % possible all: 50.2
Reflection
*PLUS
Num. measured all: 240634
Reflection shell
*PLUS
% possible obs: 50.2 % / Mean I/σ(I) obs: 3.38

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→12 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: bulk solvent model used
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2629 8.1 %RANDOM
Rwork0.17 ---
obs0.17 32637 88.1 %-
all-32637 --
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.7→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 25 368 2985
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.94
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 272 7.7 %
Rwork0.328 3270 -
obs--58.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PO4.PARPO4.TOP
X-RAY DIFFRACTION3GOL.PARGOL.TOP
X-RAY DIFFRACTION4PNP.PARPNP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.94

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