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- PDB-3n8i: Crystal structure of the A isoform of human cytoplasmic protein t... -

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Basic information

Entry
Database: PDB / ID: 3n8i
TitleCrystal structure of the A isoform of human cytoplasmic protein tyrosine phosphatase (HCPTP-A) in complex with 1-naphtylacetic acid
ComponentsLow molecular weight phosphotyrosine protein phosphatase
KeywordsHYDROLASE / tyrosine phosphatase / protein-ligand complex
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 / SH3 domain binding / chemical synaptic transmission / cytoplasmic side of plasma membrane / synapse / extracellular exosome / 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 / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NAPHTHALEN-1-YL-ACETIC ACID / Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHoman, K.T. / Balasubramaniam, D. / Stauffacher, C.V.
CitationJournal: To be Published
Title: Structural Characterization of a Secondary Binding Site on Low Molecular Weight Protein Tyrosine Phosphatases
Authors: Homan, K.T. / Balasubramaniam, D. / Stauffacher, C.V.
History
DepositionMay 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,1212
Polymers17,9341
Non-polymers1861
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.46, 56.09, 95.99
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 Low molecular weight phosphotyrosine protein phosphatase / LMW-PTPase / LMW-PTP / Low molecular weight cytosolic acid phosphatase / Red cell acid phosphatase ...LMW-PTPase / LMW-PTP / Low molecular weight cytosolic acid phosphatase / Red cell acid phosphatase 1 / Adipocyte acid phosphatase


Mass: 17934.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACP1, APC1 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: P24666, protein-tyrosine-phosphatase, acid phosphatase
#2: Chemical ChemComp-NLA / NAPHTHALEN-1-YL-ACETIC ACID


Mass: 186.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22.5% PEG 3350, 0.1M TRIS pH 7.5, 10mM 1-naphthylacetic acid, 2% isopropanol, 1mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.968 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 20, 2009 / Details: SI(111) double crystal monochromator
RadiationMonochromator: SI(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 27538 / Num. obs: 27270 / % possible obs: 99.03 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 122.9 / Redundancy: 12.2 % / Biso Wilson estimate: 19.291 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 15.02
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 4.71 / Num. unique all: 2738 / % possible all: 96.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0063refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5PNT

5pnt


Resolution: 1.5→32.46 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.36 / SU ML: 0.041 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1464 5.1 %RANDOM
Rwork0.174 ---
obs0.175 27270 99.03 %-
all-27537 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.291 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→32.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 14 209 1452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221353
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.9631837
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3365173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6922465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73515245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0961511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211060
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7941.5828
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36221352
X-RAY DIFFRACTIONr_scbond_it1.9613525
X-RAY DIFFRACTIONr_scangle_it2.9334.5485
X-RAY DIFFRACTIONr_rigid_bond_restr1.0431353
X-RAY DIFFRACTIONr_sphericity_free3.0173209
X-RAY DIFFRACTIONr_sphericity_bonded2.15231319
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 106 -
Rwork0.186 1909 -
obs-2120 94.6 %
Refinement TLS params.Method: refined / Origin x: -2.675 Å / Origin y: 4.731 Å / Origin z: -10.382 Å
111213212223313233
T0.0362 Å2-0.0019 Å20.0033 Å2-0.002 Å2-0.0066 Å2--0.0276 Å2
L0.4676 °2-0.0889 °20.0931 °2-0.3074 °2-0.1588 °2--0.8757 °2
S0.0172 Å °0.0059 Å °0.0017 Å °-0.0311 Å °-0.0003 Å °-0.0083 Å °0.1235 Å °0.0118 Å °-0.0169 Å °

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