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- PDB-2yd4: Crystal structure of the N-terminal Ig1-2 module of Chicken Recep... -

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Basic information

Entry
Database: PDB / ID: 2yd4
TitleCrystal structure of the N-terminal Ig1-2 module of Chicken Receptor Protein Tyrosine Phosphatase Sigma
ComponentsPROTEIN-TYROSINE PHOSPHATASE CRYPALPHA1 ISOFORM
KeywordsHYDROLASE
Function / homology
Function and homology information


negative regulation of collateral sprouting / negative regulation of axon regeneration / negative regulation of dendritic spine development / synaptic membrane adhesion / negative regulation of axon extension / heparan sulfate proteoglycan binding / peptidyl-tyrosine dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / postsynaptic density membrane ...negative regulation of collateral sprouting / negative regulation of axon regeneration / negative regulation of dendritic spine development / synaptic membrane adhesion / negative regulation of axon extension / heparan sulfate proteoglycan binding / peptidyl-tyrosine dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / postsynaptic density membrane / synaptic vesicle membrane / heparin binding / growth cone / perikaryon / axon / signal transduction / protein homodimerization activity / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...: / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set 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 / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Receptor-type tyrosine-protein phosphatase S / Receptor-type tyrosine-protein phosphatase S
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsColes, C.H. / Shen, Y. / Tenney, A.P. / Siebold, C. / Sutton, G.C. / Lu, W. / Gallagher, J.T. / Jones, E.Y. / Flanagan, J.G. / Aricescu, A.R.
CitationJournal: Science / Year: 2011
Title: Proteoglycan-Specific Molecular Switch for Rptp Sigma Clustering and Neuronal Extension.
Authors: Coles, C.H. / Shen, Y. / Tenney, A.P. / Siebold, C. / Sutton, G.C. / Lu, W. / Gallagher, J.T. / Jones, E.Y. / Flanagan, J.G. / Aricescu, A.R.
History
DepositionMar 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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 CRYPALPHA1 ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6516
Polymers23,1571
Non-polymers4945
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.745, 104.745, 94.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-2081-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PROTEIN-TYROSINE PHOSPHATASE CRYPALPHA1 ISOFORM / RPTP / RECEPTOR PROTEIN TYROSINE PHOSPHATASE SIGMA


Mass: 23156.998 Da / Num. of mol.: 1 / Fragment: IG1-2, RESIDUES 29-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human)
References: UniProt: Q90815, UniProt: F1NWE3*PLUS, protein-tyrosine-phosphatase

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Non-polymers , 5 types, 284 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND THE C- TERMINAL NINE AMINO ACID RESIDUES ...THE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND THE C- TERMINAL NINE AMINO ACID RESIDUES (GTKHHHHHH) DERIVE FROM THE PHLSEC VECTOR.

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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: 2.8 Å3/Da / Density % sol: 57 %
Description: THE STRUCTURE WAS DETERMINED BY SAD ANALYSIS USING DATA COLLECTED FROM A SELENOMETHIONINE LABELLED PROTEIN CRYSTAL WHICH DIFFRACTED TO 3.1A
Crystal growpH: 9.6 / Details: 20% W/V PEG 8000, 0.1M CHES, PH 9.6 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9763
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.65→74 Å / Num. obs: 31882 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 26 % / Biso Wilson estimate: 17.51 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 26.2
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 18.6 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0077refinement
xia2data reduction
XDSdata reduction
xia2data scaling
SCALAdata scaling
SHELXDVIA AUTOSHARP INTERFACEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.65→74.07 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.951 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20229 1623 5.1 %RANDOM
Rwork0.17964 ---
obs0.18079 30242 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.706 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.65→74.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1567 0 30 279 1876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221746
X-RAY DIFFRACTIONr_bond_other_d0.0020.021237
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9742384
X-RAY DIFFRACTIONr_angle_other_deg0.8323.0053028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4925231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74324.18974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53115296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8271513
X-RAY DIFFRACTIONr_chiral_restr0.0860.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211972
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02331
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 108 -
Rwork0.308 2207 -
obs--99.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9244-1.2512-0.28951.6887-0.10961.0242-0.0034-0.0848-0.31910.0727-0.05260.05970.14170.15130.05590.03810.0014-0.00030.04760.01650.028517.56210.35619.5092
21.63231.2336-0.70453.6145-1.23971.99560.0478-0.05-0.0238-0.1686-0.08750.09470.0189-0.18410.03970.02310.0125-0.01260.045-0.01360.008731.87019.37942.8298
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 130
2X-RAY DIFFRACTION2A131 - 231

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