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- PDB-2ahs: Crystal Structure of the Catalytic Domain of Human Tyrosine Recep... -

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Basic information

Entry
Database: PDB / ID: 2ahs
TitleCrystal Structure of the Catalytic Domain of Human Tyrosine Receptor Phosphatase Beta
ComponentsReceptor-type tyrosine-protein phosphatase beta
KeywordsHYDROLASE / Tyrosine Receptor Phosphatase / Beta / Human / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / dephosphorylation / tertiary granule membrane / specific granule membrane / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity ...glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / dephosphorylation / tertiary granule membrane / specific granule membrane / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / osteoblast differentiation / angiogenesis / receptor complex / cadherin binding / Neutrophil degranulation / plasma membrane
Similarity search - Function
PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic ...PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / 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
Receptor-type tyrosine-protein phosphatase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsUgochukwu, E. / Eswaran, J. / Barr, A. / Gileadi, O. / Sobott, F. / Burgess, N. / Ball, L. / Bray, J. / von Delft, F. / Debreczeni, J. ...Ugochukwu, E. / Eswaran, J. / Barr, A. / Gileadi, O. / Sobott, F. / Burgess, N. / Ball, L. / Bray, J. / von Delft, F. / Debreczeni, J. / Bunkoczi, G. / Turnbull, A. / Das, S. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Large-scale structural analysis of the classical human protein tyrosine phosphatome.
Authors: Barr, A.J. / Ugochukwu, E. / Lee, W.H. / King, O.N. / Filippakopoulos, P. / Alfano, I. / Savitsky, P. / Burgess-Brown, N.A. / Muller, S. / Knapp, S.
History
DepositionJul 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2012Group: Database references
Revision 1.4Aug 23, 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_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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: Receptor-type tyrosine-protein phosphatase beta
B: Receptor-type tyrosine-protein phosphatase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,95220
Polymers68,1132
Non-polymers83918
Water8,629479
1
A: Receptor-type tyrosine-protein phosphatase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4349
Polymers34,0561
Non-polymers3788
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-type tyrosine-protein phosphatase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,51711
Polymers34,0561
Non-polymers46110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.368, 123.368, 179.569
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLYSLYS5AA1705 - 174529 - 69
21LYSLYSLYSLYS5BB1705 - 174529 - 69
32ASPASPGLNGLN5AA1756 - 180380 - 127
42ASPASPGLNGLN5BB1756 - 180380 - 127
53CYSCYSVALVAL6AA1804 - 1810128 - 134
63CYSCYSVALVAL6BB1804 - 1810128 - 134
74LYSLYSTRPTRP5AA1811 - 1816135 - 140
84LYSLYSTRPTRP5BB1811 - 1816135 - 140
95PROPROSERSER6AA1817 - 1822141 - 146
105PROPROSERSER6BB1817 - 1822141 - 146
116LEULEUGLUGLU5AA1823 - 1851147 - 175
126LEULEUGLUGLU5BB1823 - 1851147 - 175
137ASPASPPROPRO5AA1855 - 1869179 - 193
147ASPASPPROPRO5BB1855 - 1869179 - 193
158HISHISLYSLYS5AA1871 - 1927195 - 251
168HISHISLYSLYS5BB1871 - 1927195 - 251
179VALVALASPASP5AA1930 - 1962254 - 286
189VALVALASPASP5BB1930 - 1962254 - 286

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase beta / Protein-tyrosine phosphatase beta / R-PTP-beta


Mass: 34056.469 Da / Num. of mol.: 2 / Fragment: PTPR-beta
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRB, PTPB / Plasmid: pGEX-6P2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-R3 / References: UniProt: P23467, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.9 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 277 K / pH: 7
Details: PEG6000, Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9787
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.1→53.4 Å / Num. obs: 47341 / % possible obs: 99.2 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.21 Å / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RPM.PDB

1rpm


Resolution: 2.1→53.4 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.573 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2394 5.1 %RANDOM
Rwork0.152 ---
obs0.155 44882 99.2 %-
all-44882 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.09 Å20 Å2
2---0.19 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.1→53.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4444 0 42 479 4965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214643
X-RAY DIFFRACTIONr_bond_other_d0.0010.024128
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.9396311
X-RAY DIFFRACTIONr_angle_other_deg0.89539554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3125570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21123.444241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22315759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0631541
X-RAY DIFFRACTIONr_chiral_restr0.1210.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025215
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02984
X-RAY DIFFRACTIONr_nbd_refined0.2020.2853
X-RAY DIFFRACTIONr_nbd_other0.1860.24201
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22226
X-RAY DIFFRACTIONr_nbtor_other0.0810.22585
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2344
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4670.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.03852785
X-RAY DIFFRACTIONr_mcbond_other2.00351127
X-RAY DIFFRACTIONr_mcangle_it6.75274525
X-RAY DIFFRACTIONr_scbond_it9.51891936
X-RAY DIFFRACTIONr_scangle_it11.135111776
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1340medium positional0.180.5
2271loose positional0.545
1340medium thermal1.352
2271loose thermal3.310
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 173 -
Rwork0.183 3024 -
obs--92.61 %
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)
11.2860.3136-0.26531.0774-0.07780.98230.1592-0.2335-0.04830.2038-0.1440.071-0.05190.0698-0.0152-0.0885-0.0393-0.0015-0.0046-0.04-0.10827.682968.37226.6808
21.70620.2407-0.3891.0150.23471.42740.0105-0.2621-0.22490.16050.022-0.06350.22880.0189-0.0325-0.0722-0.0088-0.0216-0.01670.0408-0.0586.252535.44691.3754
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 291
2X-RAY DIFFRACTION2B17 - 290

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