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- PDB-2nv5: Crystal structure of a C-terminal phosphatase domain of Rattus no... -

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Basic information

Entry
Database: PDB / ID: 2nv5
TitleCrystal structure of a C-terminal phosphatase domain of Rattus norvegicus ortholog of human protein tyrosine phosphatase, receptor type, D (PTPRD)
Componentsprotein-tyrosine-phosphatase
KeywordsHYDROLASE / PHOSPHATASE / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Receptor-type tyrosine-protein phosphatases / negative regulation of toll-like receptor 9 signaling pathway / trans-synaptic signaling / trans-synaptic signaling by trans-synaptic complex / negative regulation of interferon-alpha production / chondroitin sulfate binding / negative regulation of collateral sprouting / presynaptic membrane assembly / negative regulation of axon regeneration / negative regulation of dendritic spine development ...Receptor-type tyrosine-protein phosphatases / negative regulation of toll-like receptor 9 signaling pathway / trans-synaptic signaling / trans-synaptic signaling by trans-synaptic complex / negative regulation of interferon-alpha production / chondroitin sulfate binding / negative regulation of collateral sprouting / presynaptic membrane assembly / negative regulation of axon regeneration / negative regulation of dendritic spine development / establishment of endothelial intestinal barrier / synaptic membrane adhesion / negative regulation of axon extension / presynapse assembly / corpus callosum development / positive regulation of dendritic spine morphogenesis / regulation of postsynaptic density assembly / negative regulation of receptor signaling pathway via JAK-STAT / positive regulation of dendrite morphogenesis / negative regulation of interferon-beta production / heparan sulfate proteoglycan binding / positive regulation of synapse assembly / Synaptic adhesion-like molecules / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / spinal cord development / phosphoprotein phosphatase activity / regulation of immune response / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / cerebellum development / hippocampal mossy fiber to CA3 synapse / hippocampus development / modulation of chemical synaptic transmission / synapse organization / postsynaptic density membrane / Schaffer collateral - CA1 synapse / cerebral cortex development / synaptic vesicle membrane / neuron differentiation / heparin binding / presynaptic membrane / negative regulation of neuron projection development / growth cone / cellular response to hypoxia / perikaryon / axon / signaling receptor binding / glutamatergic synapse / signal transduction / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 ...Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Tyrosine specific protein phosphatases domain profile. / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
protein-tyrosine-phosphatase / Receptor-type tyrosine-protein phosphatase S
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBonanno, J.B. / Gilmore, J. / Bain, K.T. / Iizuka, M. / Xu, W. / Wasserman, S. / Smith, D. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2007
Title: Structural genomics of protein phosphatases.
Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. ...Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. / Ragumani, S. / Patskovsky, Y. / Alvarado, J. / Ramagopal, U.A. / Faber-Barata, J. / Chance, M.R. / Sali, A. / Fiser, A. / Zhang, Z.Y. / Lawrence, D.S. / Burley, S.K.
History
DepositionNov 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.6Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.7Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.8Oct 2, 2024Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_host_org_vector_type / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein-tyrosine-phosphatase
B: protein-tyrosine-phosphatase
C: protein-tyrosine-phosphatase


Theoretical massNumber of molelcules
Total (without water)103,0373
Polymers103,0373
Non-polymers00
Water11,313628
1
A: protein-tyrosine-phosphatase


Theoretical massNumber of molelcules
Total (without water)34,3461
Polymers34,3461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: protein-tyrosine-phosphatase


Theoretical massNumber of molelcules
Total (without water)34,3461
Polymers34,3461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: protein-tyrosine-phosphatase


Theoretical massNumber of molelcules
Total (without water)34,3461
Polymers34,3461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.789, 140.789, 112.431
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein protein-tyrosine-phosphatase / PTPRD


Mass: 34345.742 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ptprd / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: M0RB22, UniProt: Q64605*PLUS, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 30% PEG MME 2K, 100mM potassium thiocyanate, pH 7.0, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 2, 2006
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2→19.89 Å / Num. all: 85072 / Num. obs: 83626 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.5 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 18
Reflection shellResolution: 2→2.11 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 3.4 / Num. measured all: 149687 / Num. unique all: 11897 / Rsym value: 0.837 / % possible all: 96.3

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.89 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.853 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.158 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.237 4119 4.9 %RANDOM
Rwork0.197 ---
obs0.199 83277 97.98 %-
all-84994 --
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: 34.197 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6861 0 0 628 7489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227056
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9379595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8735854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20523.577355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.443151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4621554
X-RAY DIFFRACTIONr_chiral_restr0.1050.21039
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025465
X-RAY DIFFRACTIONr_nbd_refined0.2040.23028
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24812
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2524
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.225
X-RAY DIFFRACTIONr_mcbond_it1.0311.54383
X-RAY DIFFRACTIONr_mcangle_it1.62426921
X-RAY DIFFRACTIONr_scbond_it2.4833069
X-RAY DIFFRACTIONr_scangle_it3.7914.52670
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 310 -
Rwork0.236 5648 -
obs-5958 95.74 %

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