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- PDB-7cuy: Crystal structure of Primo-1 -

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Basic information

Entry
Database: PDB / ID: 7cuy
TitleCrystal structure of Primo-1
ComponentsLow molecular weight phosphotyrosine protein phosphatase 1
KeywordsHYDROLASE / LMW-PTP / LMWPTP / Primo-1
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / nucleus / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, low molecular weight, mammalian / : / 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
Similarity search - Domain/homology
Low molecular weight phosphotyrosine protein phosphatase 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.081 Å
AuthorsLee, H.S. / Kim, S.J. / Ku, B.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future Planning (MSIP)2019M3E5D6063955 Korea, Republic Of
CitationJournal: Mol.Cells / Year: 2020
Title: Structural and Biochemical Characterization of the Two Drosophila Low Molecular Weight-Protein Tyrosine Phosphatases DARP and Primo-1.
Authors: Lee, H.S. / Mo, Y. / Shin, H.C. / Kim, S.J. / Ku, B.
History
DepositionAug 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Low molecular weight phosphotyrosine protein phosphatase 1
B: Low molecular weight phosphotyrosine protein phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7844
Polymers37,3072
Non-polymers4772
Water2,216123
1
A: Low molecular weight phosphotyrosine protein phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8922
Polymers18,6541
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Low molecular weight phosphotyrosine protein phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8922
Polymers18,6541
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.921, 59.902, 60.925
Angle α, β, γ (deg.)90.000, 110.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Low molecular weight phosphotyrosine protein phosphatase 1 / Low molecular weight cytosolic acid phosphatase 1 / PTPase 1


Mass: 18653.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: primo-1, CG31311 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P82890, protein-tyrosine-phosphatase, acid 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES-NaOH (pH 7.47), 1.2 M sodium citrate tribasic, 9% (w/v) D-sorbitol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.081→50 Å / Num. obs: 18049 / % possible obs: 97.4 % / Redundancy: 4.7 % / CC1/2: 0.983 / Rsym value: 0.095 / Net I/σ(I): 23.8
Reflection shellResolution: 2.081→2.14 Å / Num. unique obs: 839 / CC1/2: 0.832 / Rsym value: 0.252

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5got

5got


Resolution: 2.081→29.81 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.54 / Phase error: 23.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 1793 9.94 %
Rwork0.1795 16247 -
obs0.1855 18040 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.67 Å2 / Biso mean: 29.6046 Å2 / Biso min: 13.59 Å2
Refinement stepCycle: final / Resolution: 2.081→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 30 123 2549
Biso mean--30.66 32.9 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082462
X-RAY DIFFRACTIONf_angle_d0.9543307
X-RAY DIFFRACTIONf_chiral_restr0.052361
X-RAY DIFFRACTIONf_plane_restr0.005426
X-RAY DIFFRACTIONf_dihedral_angle_d16.0241515
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0813-2.13750.28771140.2319102080
2.1375-2.20040.30071340.2372122796
2.2004-2.27140.32591410.2175122795
2.2714-2.35250.27091310.2037122695
2.3525-2.44670.26761400.1994124696
2.4467-2.5580.29191400.2071124797
2.558-2.69280.27191390.2021127197
2.6928-2.86130.26181480.1871126999
2.8613-3.08210.25871370.1902128999
3.0821-3.39180.22461410.1752128399
3.3918-3.88170.21011420.1509130499
3.8817-4.88710.19141380.137129299
4.8871-29.810.20511480.1768134699

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