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- PDB-2vph: Crystal structure of the human protein tyrosine phosphatase, non-... -

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Basic information

Entry
Database: PDB / ID: 2vph
TitleCrystal structure of the human protein tyrosine phosphatase, non- receptor type 4, PDZ domain
ComponentsTYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 4
KeywordsHYDROLASE / PROTEIN PHOSPHATASE / PTPN4 / PTPMEG / CYTOSKELETON / MEGAKARYOCYTE / DEPHOSPHORYLATION / STRUCTURAL PROTEIN
Function / homology
Function and homology information


Toll Like Receptor 4 (TLR4) Cascade / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / glutamate receptor binding / MECP2 regulates neuronal receptors and channels / cytoskeletal protein binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane ...Toll Like Receptor 4 (TLR4) Cascade / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / glutamate receptor binding / MECP2 regulates neuronal receptors and channels / cytoskeletal protein binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / cytoskeleton / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain ...Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / PDZ domain / Pdz3 Domain / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / 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 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRoos, A.K. / Wang, J. / Burgess-Brown, N. / Elkins, J.M. / Kavanagh, K. / Pike, A.C.W. / Filippakopoulos, P. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. ...Roos, A.K. / Wang, J. / Burgess-Brown, N. / Elkins, J.M. / Kavanagh, K. / Pike, A.C.W. / Filippakopoulos, P. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Bountra, C. / Knapp, S.
CitationJournal: To be Published
Title: Crystal Structure of the Human Protein Tyrosine Phosphatase, Non-Receptor Type 4, Pdz Domain
Authors: Roos, A.K. / Wang, J. / Burgess-Brown, N. / Elkins, J.M. / Kavanagh, K. / Pike, A.C.W. / Filippakopoulos, P. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Bountra, C. / Knapp, S.
History
DepositionFeb 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 4
B: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 4


Theoretical massNumber of molelcules
Total (without water)22,0812
Polymers22,0812
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-4.5 kcal/mol
Surface area12340 Å2
MethodPQS
2
A: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 4


Theoretical massNumber of molelcules
Total (without water)11,0411
Polymers11,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 4


Theoretical massNumber of molelcules
Total (without water)11,0411
Polymers11,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.489, 71.015, 71.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUASPASPAA515 - 5545 - 44
21LEULEUASPASPBB515 - 5545 - 44
12CYSCYSALAALAAA556 - 58846 - 78
22CYSCYSALAALABB556 - 58846 - 78
13GLUGLUGLUGLUAA596 - 60786 - 97
23GLUGLUGLUGLUBB596 - 60786 - 97

NCS oper: (Code: given
Matrix: (0.992, 0.037, -0.117), (0.118, -0.022, 0.993), (0.034, -0.999, -0.027)
Vector: -8.44412, 15.433, 17.8965)

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Components

#1: Protein TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 4 / PROTEIN-TYROSINE PHOSPHATASE MEG1 / PTPASE-MEG1 / MEG


Mass: 11040.697 Da / Num. of mol.: 2 / Fragment: PDZ DOMAIN, RESIDUES 513-606
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-ROSETTA-PRARE2 / References: UniProt: P29074, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.09 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 5 / Details: 20% PEG 3350, 0.20M (NH4)2H(CIT), PH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98068
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98068 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 15306 / % possible obs: 100 % / Observed criterion σ(I): 2.8 / Redundancy: 7 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2OCS, 2HE2, 1QAV

2ocs

2he2

1qav


Resolution: 1.9→45 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.694 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 765 5 %RANDOM
Rwork0.208 ---
obs0.21 14492 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å20 Å2
2---0.9 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 0 72 1496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221444
X-RAY DIFFRACTIONr_bond_other_d0.0040.02949
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.981963
X-RAY DIFFRACTIONr_angle_other_deg0.92132327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4145186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52624.60363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.30815233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3041511
X-RAY DIFFRACTIONr_chiral_restr0.080.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211619
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02264
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_it2.8613945
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.23551522
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.8898499
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.36611441
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A491medium positional0.150.5
2B491medium positional0.150.5
1A547loose positional0.215
2B547loose positional0.215
1A491medium thermal1.192
2B491medium thermal1.192
1A547loose thermal1.1510
2B547loose thermal1.1510
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.347 51
Rwork0.255 1059
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)
12.029-0.63620.54092.7036-1.2294.42660.0713-0.0628-0.01430.0590.14840.11320.069-0.1328-0.2197-0.07460.0159-0.0276-0.1158-0.0103-0.073316.735819.570417.6481
21.57541.01270.45982.70181.12536.7214-0.06250.06070.0648-0.0199-0.01540.1460.0812-0.51970.0778-0.0635-0.0025-0.0297-0.06290.0172-0.05117.894733.9617-2.0656
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A513 - 610
2X-RAY DIFFRACTION2B513 - 610

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