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- PDB-3ng8: Crystal structure of an abridged SER TO ALA MUTANT OF THE MATURE ... -

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Basic information

Entry
Database: PDB / ID: 3ng8
TitleCrystal structure of an abridged SER TO ALA MUTANT OF THE MATURE ECTODOMAIN of the human receptor-type protein-tyrosine phosphatase ICA512/IA-2 at PH 8.5
ComponentsReceptor-type tyrosine-protein phosphatase-like N
KeywordsTRANSFERASE / IA-2 / ICA-512 / PROTEIN-TYROSINE PHOSPHATASE / TRANSMEMBRANE PROTEIN / DIABETES / AUTOIMMUNITY / PROTEOLYSIS / GLYCOPROTEIN / RECEPTOR
Function / homology
Function and homology information


dense core granule maturation / regulation of secretion / luteinization / positive regulation of type B pancreatic cell proliferation / insulin secretion involved in cellular response to glucose stimulus / insulin secretion / transport vesicle membrane / spectrin binding / transcription factor binding / ubiquitin-like protein ligase binding ...dense core granule maturation / regulation of secretion / luteinization / positive regulation of type B pancreatic cell proliferation / insulin secretion involved in cellular response to glucose stimulus / insulin secretion / transport vesicle membrane / spectrin binding / transcription factor binding / ubiquitin-like protein ligase binding / axon terminus / secretory granule / response to reactive oxygen species / perikaryon / endosome / neuronal cell body / synapse / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleus / plasma membrane
Similarity search - Function
Protein-tyrosine phosphatase receptor IA-2 ectodomain / Protein-tyrosine phosphatase receptor IA-2 ectodomain / RESP18 domain / Receptor-type tyrosine-protein phosphatase-like N/N2 / Protein-tyrosine phosphatase receptor IA-2, ectodomain superfamily / Protein-tyrosine phosphatase receptor IA-2 / RESP18 domain / RESP18 / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. ...Protein-tyrosine phosphatase receptor IA-2 ectodomain / Protein-tyrosine phosphatase receptor IA-2 ectodomain / RESP18 domain / Receptor-type tyrosine-protein phosphatase-like N/N2 / Protein-tyrosine phosphatase receptor IA-2, ectodomain superfamily / Protein-tyrosine phosphatase receptor IA-2 / RESP18 domain / RESP18 / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase-like N
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsPrimo, M.E. / Jakoncic, J. / Poskus, E. / Ermacora, M.R.
Citation
Journal: J.Biol.Chem. / Year: 2008
Title: Structure of the mature ectodomain of the human receptor-type protein-tyrosine phosphatase IA-2.
Authors: Primo, M.E. / Klinke, S. / Sica, M.P. / Goldbaum, F.A. / Jakoncic, J. / Poskus, E. / Ermacora, M.R.
#1: Journal: J.Biol.Chem. / Year: 2008
Title: Structure of the Mature Ectodomain of the Human Receptor-Type Protein-Tyrosine Phosphatase Ia-2
Authors: Primo, M.E. / Klinke, S. / Sica, M.P. / Goldbaum, F.A. / Jakoncic, J. / Poskus, E. / Ermacora, M.R.
History
DepositionJun 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: Receptor-type tyrosine-protein phosphatase-like N
B: Receptor-type tyrosine-protein phosphatase-like N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2843
Polymers19,2442
Non-polymers401
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-type tyrosine-protein phosphatase-like N
hetero molecules

A: Receptor-type tyrosine-protein phosphatase-like N


Theoretical massNumber of molelcules
Total (without water)19,2843
Polymers19,2442
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area1100 Å2
ΔGint-14 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.554, 66.544, 73.712
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 Receptor-type tyrosine-protein phosphatase-like N / R-PTP-N / PTP IA-2 / Islet cell antigen 512 / ICA 512 / Islet cell autoantigen 3


Mass: 9621.916 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 470-558 / Mutation: S508A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ICA3, ICA512, PTPRN / Plasmid: PET9B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q16849
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% (W/V) PEG 4000, 0.1 M TrisCl PH 8.5, 0.2 M CACL2, VAPOR DIFFUSION, HANGING DROP, temperature 292

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0332
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 15, 2010 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI (111) CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.35→20 Å / Num. obs: 34457 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 44.2
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3 / Rsym value: 0.28 / % possible all: 85.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QT7

2qt7


Resolution: 1.35→19.45 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.014 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22394 1735 5 %RANDOM
Rwork0.17694 ---
obs0.17934 32636 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.718 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2--0.09 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.35→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 1 215 1528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221445
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9711984
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6665208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79826.39361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46615268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.31154
X-RAY DIFFRACTIONr_chiral_restr0.1070.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021072
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_it1.841.5919
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.90321496
X-RAY DIFFRACTIONr_scbond_it3.8853526
X-RAY DIFFRACTIONr_scangle_it5.8074.5470
X-RAY DIFFRACTIONr_rigid_bond_restr1.78631445
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 133 -
Rwork0.298 2122 -
obs--100 %

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