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- PDB-2pi7: Structure of the catalytic domain of the chick retinal neurite in... -

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Basic information

Entry
Database: PDB / ID: 2pi7
TitleStructure of the catalytic domain of the chick retinal neurite inhibitor-Receptor Protein Tyrosine Phosphatase CRYP-2/cPTPRO
ComponentsProtein tyrosine phosphatase CRYP-2
KeywordsHYDROLASE / Protein Tyrosine Phosphatase
Function / homology
Function and homology information


slit diaphragm assembly / negative regulation of retinal ganglion cell axon guidance / regulation of glomerular filtration / negative regulation of glomerular filtration / podocyte differentiation / Wnt-protein binding / glomerulus development / motor neuron axon guidance / negative regulation of cell-substrate adhesion / lamellipodium assembly ...slit diaphragm assembly / negative regulation of retinal ganglion cell axon guidance / regulation of glomerular filtration / negative regulation of glomerular filtration / podocyte differentiation / Wnt-protein binding / glomerulus development / motor neuron axon guidance / negative regulation of cell-substrate adhesion / lamellipodium assembly / monocyte chemotaxis / peptidyl-tyrosine dephosphorylation / lateral plasma membrane / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / axon guidance / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / negative regulation of neuron projection development / lamellipodium / growth cone / membrane => GO:0016020 / dendritic spine / neuron projection / apical plasma membrane / axon / protein homodimerization activity / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase O / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. ...Receptor-type tyrosine-protein phosphatase O / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase / 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 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsGirish, T.S. / Gopal, B.
CitationJournal: Proteins / Year: 2007
Title: The crystal structure of the catalytic domain of the chick retinal neurite inhibitor-receptor protein tyrosine phosphatase CRYP-2/cPTPRO
Authors: Girish, T.S. / Gopal, B.
History
DepositionApr 13, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 25, 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: Protein tyrosine phosphatase CRYP-2
B: Protein tyrosine phosphatase CRYP-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3674
Polymers73,2432
Non-polymers1242
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.316, 68.316, 245.018
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein tyrosine phosphatase CRYP-2


Mass: 36621.637 Da / Num. of mol.: 2 / Fragment: Catalytic Domain, Residues 956-1267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CRYP2 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Polymerase / References: UniProt: Q98945
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% PEG 10000, 0.6M Ammonium Nitrate, 125mM NaCl, 25mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.59→42.56 Å / Num. obs: 21113 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.1161 / Net I/σ(I): 10
Reflection shellResolution: 2.59→2.73 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2531

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
CNSrefinement
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RPM

1rpm


Resolution: 2.59→42.56 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2869 1063 -RANDOM
Rwork0.2268 ---
all-21575 --
obs-21002 97.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.879 Å2-1.367 Å20 Å2
2---0.879 Å20 Å2
3---1.757 Å2
Refinement stepCycle: LAST / Resolution: 2.59→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4730 0 8 182 4920
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d1.14

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