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- PDB-2i5x: Engineering the PTPbeta catalytic domain with improved crystalliz... -

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Basic information

Entry
Database: PDB / ID: 2i5x
TitleEngineering the PTPbeta catalytic domain with improved crystallization properties
ComponentsReceptor-type tyrosine-protein phosphatase beta
KeywordsHYDROLASE / protein tyrosine phosphatase / WPD-loop / drug design / protein engineering
Function / homology
Function and homology information


glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / dephosphorylation / tertiary granule membrane / protein dephosphorylation / specific granule membrane / protein-tyrosine-phosphatase / osteoblast differentiation / angiogenesis ...glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / dephosphorylation / tertiary granule membrane / protein dephosphorylation / specific granule membrane / protein-tyrosine-phosphatase / 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 profile. / Tyrosine-specific protein phosphatases domain / 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
(4-ETHYLPHENYL)SULFAMIC ACID / Receptor-type tyrosine-protein phosphatase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsEvdokimov, A.G. / Pokross, M.E. / Walter, R.L. / Mekel, M. / Klopfenstein, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Engineering the catalytic domain of human protein tyrosine phosphatase beta for structure-based drug discovery.
Authors: Evdokimov, A.G. / Pokross, M. / Walter, R. / Mekel, M. / Cox, B. / Li, C. / Bechard, R. / Genbauffe, F. / Andrews, R. / Diven, C. / Howard, B. / Rastogi, V. / Gray, J. / Maier, M. / Peters, K.G.
History
DepositionAug 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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_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.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_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)73,0747
Polymers72,5762
Non-polymers4985
Water5,873326
1
A: Receptor-type tyrosine-protein phosphatase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5253
Polymers36,2881
Non-polymers2372
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)36,5494
Polymers36,2881
Non-polymers2613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.973, 71.308, 69.690
Angle α, β, γ (deg.)90.00, 93.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36288.035 Da / Num. of mol.: 2 / Fragment: catalytic domain, residues 1662-1973
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRB, PTPB / Plasmid: pDEST-HisMBP / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P23467, protein-tyrosine-phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UA5 / (4-ETHYLPHENYL)SULFAMIC ACID


Mass: 201.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11NO3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 21% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2004 / Details: Si monochromator
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→39.6 Å / Num. all: 66068 / Num. obs: 66068 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 20.73 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.98
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.64 / Num. unique all: 9811 / % possible all: 97.9

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I4h

2i4h


Resolution: 1.7→39.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.633 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: TLS-one group per polypeptide chain
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.107 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 3354 5.1 %RANDOM
Rwork0.179 ---
all0.181 66068 --
obs0.18 66068 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20.25 Å2
2---0.68 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4582 0 29 326 4937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224815
X-RAY DIFFRACTIONr_angle_refined_deg0.921.9466555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4945587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8723.36247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98515829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3991542
X-RAY DIFFRACTIONr_chiral_restr0.0860.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023706
X-RAY DIFFRACTIONr_nbd_refined0.2310.22292
X-RAY DIFFRACTIONr_nbtor_refined0.320.23288
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2268
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2850.242
X-RAY DIFFRACTIONr_mcbond_it1.6511.52895
X-RAY DIFFRACTIONr_mcangle_it2.55724646
X-RAY DIFFRACTIONr_scbond_it3.71932156
X-RAY DIFFRACTIONr_scangle_it5.4214.51892
LS refinement shellResolution: 1.703→1.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 231 -
Rwork0.222 4467 -
obs-4698 95.74 %
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)
10.3591-0.01990.03360.67520.13150.0724-0.00070.0110.0231-0.03780.01270.03850.0015-0.0003-0.0119-0.0278-0.0002-0.0027-0.01710.0115-0.019115.1985-11.709835.9427
20.358-0.0142-0.16010.4713-0.18220.47-0.022-0.0095-0.0001-0.0630.0032-0.03950.06380.04850.01880.0050.01250.0134-0.0209-0.007-0.0423-16.977311.63962.7541
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1678 - 196718 - 307
22BB1678 - 196918 - 309

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