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- PDB-3np5: Crystal structure of an abridged form of the mature ectodomain of... -

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Basic information

Entry
Database: PDB / ID: 3np5
TitleCrystal structure of an abridged form of the mature ectodomain of the human receptor-type protein tyrosine phosphatase ICA512/IA-2 AT pH 4.5
ComponentsReceptor-type tyrosine-protein phosphatase-like N
KeywordsHYDROLASE / IA-2 / ICA-512 / PROTEIN-TYROSINE PHOSPHATASE / TRANSMEMBRANE PROTEIN / DIABETES / AUTOIMMUNITY / PROTEOLYSIS / GLYCOPROTEIN / RECEPTOR
Function / homology
Function and homology information


dense core granule maturation / positive regulation of type B pancreatic cell proliferation / regulation of secretion / luteinization / insulin secretion involved in cellular response to glucose stimulus / insulin secretion / transport vesicle membrane / spectrin binding / ubiquitin-like protein ligase binding / transcription factor binding ...dense core granule maturation / positive regulation of type B pancreatic cell proliferation / regulation of secretion / luteinization / insulin secretion involved in cellular response to glucose stimulus / insulin secretion / transport vesicle membrane / spectrin binding / ubiquitin-like protein ligase binding / transcription factor binding / axon terminus / response to reactive oxygen species / secretory granule / perikaryon / endosome / neuronal cell body / synapse / 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 / Tyrosine specific protein phosphatases domain profile. / 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: 1.8 Å
AuthorsPrimo, M.E. / Jakoncic, J. / Poskus, E. / Ermacora, M.R.
Citation
Journal: To be Published
Title: Receptor-Type Protein-Tyrosine Phosphatase Ia-2-Ica512
Authors: Primo, M.E. / 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 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2012Group: Structure summary
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_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_asym_id / _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_asym_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_asym_id / _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_asym_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_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: Receptor-type tyrosine-protein phosphatase-like N
B: Receptor-type tyrosine-protein phosphatase-like N
C: Receptor-type tyrosine-protein phosphatase-like N
D: Receptor-type tyrosine-protein phosphatase-like N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6326
Polymers38,5524
Non-polymers802
Water2,378132
1


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

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


Theoretical massNumber of molelcules
Total (without water)19,3163
Polymers19,2762
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1080 Å2
ΔGint-7 kcal/mol
Surface area8930 Å2
MethodPISA
3
B: Receptor-type tyrosine-protein phosphatase-like N

D: Receptor-type tyrosine-protein phosphatase-like N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3163
Polymers19,2762
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area1260 Å2
ΔGint-17 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.662, 44.662, 168.665
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Receptor-type tyrosine-protein phosphatase-like N / R-PTP-N / Islet cell antigen 512 / ICA 512 / Islet cell autoantigen 3 / PTP IA-2


Mass: 9637.916 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 470-558
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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% (W/V) PEG 4000, 0.1 M AcNa/AcH, PH 4.50.2 M CALCIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 1, 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: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 28186 / Num. obs: 28186 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 40.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.226 / % possible all: 73.6

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Processing

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

2qt7


Resolution: 1.8→19.84 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23852 1390 5 %RANDOM
Rwork0.1611 ---
all0.16465 ---
obs-26639 92.06 %-
Displacement parametersBiso mean: 20.89 Å2
Baniso -1Baniso -2Baniso -3
1--4.95 Å20 Å20 Å2
2---4.95 Å20 Å2
3---9.89 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 2 132 2813
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.022
X-RAY DIFFRACTIONr_angle_refined_deg1.968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.902
X-RAY DIFFRACTIONr_chiral_restr0.2
LS refinement shellResolution: 1.8→1.846 Å
RfactorNum. reflection% reflection
Rfree0.414 66 -
Rwork0.25 --
obs-1573 74 %

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