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- PDB-1d2a: CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSIN... -

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Basic information

Entry
Database: PDB / ID: 1d2a
TitleCRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE (LTP1) COMPLEXED WITH THE ACTIVATOR ADENINE
ComponentsTYROSINE PHOSPHATASE
KeywordsHYDROLASE / BETA-ALPHA-BETA / TYROSINE PHOSPHATASE / LTP1
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / nucleus / cytoplasm
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
ADENINE / PHOSPHATE ION / Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsWang, S. / Stauffacher, C.V. / Van Etten, R.L.
Citation
Journal: Biochemistry / Year: 2000
Title: Structural and mechanistic basis for the activation of a low-molecular weight protein tyrosine phosphatase by adenine.
Authors: Wang, S. / Stauffacher, C.V. / Van Etten, R.L.
#1: Journal: To be Published
Title: Crystal Structure 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.
#2: 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 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYROSINE PHOSPHATASE
B: TYROSINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4406
Polymers37,0802
Non-polymers3614
Water5,405300
1
A: TYROSINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6703
Polymers18,5401
Non-polymers1302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TYROSINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7703
Polymers18,5401
Non-polymers2302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.492, 63.272, 97.590
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


Mass: 18539.959 Da / Num. of mol.: 2 / Mutation: C13A
Source method: isolated from a genetically manipulated source
Details: INACTIVE MUTANT OF LTP1 THAT THE NUCLEOPHILE CYSTEINE IS MUTATED TO ALANINE IS USED.
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: P40347, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Compound detailsInactive mutant of LTP1 that the nucleophile cysteine is mutated to alanine is used.

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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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 3400, Bis-TRIS, sodium chloride, sodium phosphate, adenine, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
212-18 %PEG34001reservoir
350 mM1reservoirNaCl
4100 mMbis-tris1reservoir
520 mMsodium phosphate1reservoir
620 mMadenine1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 22621 / Num. obs: 22621 / % possible obs: 87.6 % / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 35.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.149 / Num. unique all: 989 / % possible all: 39.3
Reflection
*PLUS
Num. measured all: 327192
Reflection shell
*PLUS
% possible obs: 39.3 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→12 Å / Rfactor Rfree error: 0.006 / 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
Rfree0.243 1773 7.9 %RANDOM
Rwork0.182 ---
obs0.182 22457 87.5 %-
all-22457 --
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 21 300 2869
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.79
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: 1.9→2.02 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 125 6.6 %
Rwork0.288 1766 -
obs--45.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PO4.PARPO4.TOP
X-RAY DIFFRACTION3ADE.PARADE.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.244 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.42
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.79

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