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- PDB-2yd7: Crystal structure of the N-terminal Ig1-2 module of Human Recepto... -

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Basic information

Entry
Database: PDB / ID: 2yd7
TitleCrystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase Delta
ComponentsPTPRD PROTEIN
KeywordsHYDROLASE
Function / homology
Function and homology information


trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / transmembrane receptor protein tyrosine phosphatase activity / presynapse assembly / synaptic membrane adhesion / positive regulation of dendritic spine morphogenesis / regulation of postsynaptic density assembly / Synaptic adhesion-like molecules ...trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / transmembrane receptor protein tyrosine phosphatase activity / presynapse assembly / synaptic membrane adhesion / positive regulation of dendritic spine morphogenesis / regulation of postsynaptic density assembly / Synaptic adhesion-like molecules / negative regulation of receptor signaling pathway via JAK-STAT / phosphate-containing compound metabolic process / positive regulation of synapse assembly / heterophilic cell-cell adhesion / regulation of immune response / cell adhesion molecule binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / hippocampal mossy fiber to CA3 synapse / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / neuron differentiation / presynaptic membrane / signaling receptor binding / glutamatergic synapse / signal transduction / extracellular exosome / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / : / 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 ...Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / : / 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
PHOSPHATE ION / Receptor-type tyrosine-protein phosphatase delta / Receptor-type tyrosine-protein phosphatase delta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PTPRD PROTEIN
B: PTPRD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2455
Polymers46,9602
Non-polymers2853
Water2,522140
1
A: PTPRD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5752
Polymers23,4801
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PTPRD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6703
Polymers23,4801
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.157, 31.724, 92.323
Angle α, β, γ (deg.)90.00, 111.97, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9995, 0.0203, -0.026), (0.0219, 0.9979, -0.0606), (0.0247, -0.0611, -0.9978)
Vector: 146.6695, -1.0825, 39.0915)

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Components

#1: Protein PTPRD PROTEIN / RPTPD / RECEPTOR PROTEIN TYROSINE PHOSPHATASE DELTA


Mass: 23480.199 Da / Num. of mol.: 2 / Fragment: IG1-2, RESIDUES 21-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human)
References: UniProt: Q3KPJ2, UniProt: P23468*PLUS, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growDetails: 20% W/V PEG 3350, 0.2M AMMONIUM DI-HYDROGEN PHOSPHATE .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 30633 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 29.71 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.8
Reflection shellResolution: 2→2.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0077refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YD4

2yd4


Resolution: 1.98→85.61 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.417 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CLEAR ELECTRON DENSITY IS NOT VISIBLE FOR AMINO ACID RESIDUES 170-172 CHAIN A AND 169-173 CHAIN B. THESE RESIDUES ARE NOT INCLUDED IN THIS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CLEAR ELECTRON DENSITY IS NOT VISIBLE FOR AMINO ACID RESIDUES 170-172 CHAIN A AND 169-173 CHAIN B. THESE RESIDUES ARE NOT INCLUDED IN THIS CRYSTAL STRUCTURE. ARG 220 SIDECHAINS ARE DISORDERED AND THEREFORE NOT INCLUDED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.24881 1546 5 %RANDOM
Rwork0.2188 ---
obs0.22029 29087 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.258 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å20 Å2-0.05 Å2
2--2.24 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.98→85.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3026 0 15 140 3181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223158
X-RAY DIFFRACTIONr_bond_other_d0.0010.022226
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9744299
X-RAY DIFFRACTIONr_angle_other_deg0.7523.0035408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1355406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01123.699146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43915542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6471533
X-RAY DIFFRACTIONr_chiral_restr0.0720.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02623
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: 1.982→2.034 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 111 -
Rwork0.299 2002 -
obs--95.7 %
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)
18.04320.8119-2.40631.60090.14536.251-0.03680.2084-0.407-0.0110.03140.03210.39950.32350.00540.08210.05140.01330.0489-0.0080.036660.3736-6.061822.1784
25.8316-0.13272.45242.0222-0.00437.4343-0.18310.06550.6135-0.1583-0.130.1694-0.5597-0.46550.31310.08160.0229-0.02730.0654-0.00750.169942.2996.275622.6002
310.2696-0.7263-3.09380.95670.21185.8835-0.0139-0.0706-0.57640.0623-0.0576-0.20260.3319-0.34680.07150.0897-0.00930.00840.0380.03780.11585.6062-5.655919.4762
47.70691.89752.54382.03261.14235.9257-0.219-0.00960.88420.0348-0.0226-0.0387-0.51220.36340.24170.09130.0058-0.03910.08630.04080.2873104.14686.062218.6971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 119
2X-RAY DIFFRACTION2A120 - 220
3X-RAY DIFFRACTION3B21 - 119
4X-RAY DIFFRACTION4B120 - 220

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