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- PDB-1d1p: CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSIN... -

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Basic information

Entry
Database: PDB / ID: 1d1p
TitleCRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE (LTP1)
ComponentsTYROSINE PHOSPHATASE
KeywordsHYDROLASE / BETA-ALPHA-BETA / TYROSINE PHOSPHATASE / LTP1
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / 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
Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, S. / Tabernero, L. / Zhang, M. / Harms, E. / Van Etten, R.L. / Stauffacher, 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: Version format compliance
Revision 1.3Aug 9, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,6214
Polymers37,1442
Non-polymers4772
Water1,910106
1
A: TYROSINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8102
Polymers18,5721
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TYROSINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8102
Polymers18,5721
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.586, 67.647, 115.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.156013, -0.737096, -0.657533), (-0.73758, -0.355835, 0.573897), (-0.65699, 0.574518, -0.488152)
Vector: 21.404, 21.6829, 56.6395)

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Components

#1: Protein TYROSINE PHOSPHATASE


Mass: 18572.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


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


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 3400, HEPES, sodium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
218 %PEG34001reservoir
3100 mM1reservoirNaCl
4100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 12, 1995 / Details: double focussing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 15614 / Num. obs: 15614 / % possible obs: 91.1 % / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 25.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 7.28 / Num. unique all: 1414 / Rsym value: 0.204 / % possible all: 84.6
Reflection
*PLUS
Num. measured all: 140622
Reflection shell
*PLUS
% possible obs: 84.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Bovine low molecular weight protein tyrosine phosphatase (BPTP) PDB ID: 1PNT

1pnt


Resolution: 2.2→12 Å / Rfactor Rfree error: 0.007 / 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
Rfree0.235 1061 6.8 %RANDOM
Rwork0.169 ---
obs0.169 15493 91.1 %-
all-15439 --
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 30 106 2695
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.89
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
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 159 6.8 %
Rwork0.258 2184 -
obs--83.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2HEP.PARHEP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.68
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.89

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