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- PDB-3us4: Crystal structure of a SH2 domain of a megakaryocyte-associated t... -

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Basic information

Entry
Database: PDB / ID: 3us4
TitleCrystal structure of a SH2 domain of a megakaryocyte-associated tyrosine kinase (MATK) from Homo sapiens at 1.50 A resolution
ComponentsMegakaryocyte-associated tyrosine-protein kinase
KeywordsTRANSFERASE / SH2 domain / signaling protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Downregulation of ERBB2 signaling / protein tyrosine kinase activity / protein phosphorylation / positive regulation of cell population proliferation / ATP binding / membrane / cytosol
Similarity search - Function
CSK-like, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...CSK-like, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Megakaryocyte-associated tyrosine-protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a SH2 domain of a megakaryocyte-associated tyrosine kinase (MATK) from Homo sapiens at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionNov 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references / Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Megakaryocyte-associated tyrosine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5883
Polymers11,3961
Non-polymers1922
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Megakaryocyte-associated tyrosine-protein kinase
hetero molecules

A: Megakaryocyte-associated tyrosine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1766
Polymers22,7912
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1790 Å2
ΔGint-62 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.840, 57.560, 28.750
Angle α, β, γ (deg.)90.000, 116.200, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-566-

HOH

21A-576-

HOH

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Components

#1: Protein Megakaryocyte-associated tyrosine-protein kinase / Hematopoietic consensus tyrosine-lacking kinase / Protein kinase HYL / Tyrosine-protein kinase CTK


Mass: 11395.719 Da / Num. of mol.: 1 / Fragment: SH2 domain residues 117-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTK, HYL, MATK, NM_139355 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100
References: UniProt: P42679, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 117-213) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 117-213) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. RESIDUE NUMBERING IS BASED ON UNIPROTKB ID P42679.

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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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.40M (NH4)2SO4, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999,0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2011 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.99991
20.97931
ReflectionResolution: 1.5→25.593 Å / Num. obs: 14591 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 5.02 % / Biso Wilson estimate: 23.592 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.5-1.544.760.4813.294927103693.6
1.54-1.580.3464.95226104997.8
1.58-1.630.2636.1500399696.8
1.63-1.680.2127.44979100296.2
1.68-1.730.1549.3496399197.3
1.73-1.790.10612.3452692397.5
1.79-1.860.09214.1443188498.2
1.86-1.940.07116.9423987297.4
1.94-2.020.05719.5407382397.9
2.02-2.120.05722.7435981798.4
2.12-2.240.05824408575797.2
2.24-2.370.05325.1391573498.3
2.37-2.540.0526.3356366999
2.54-2.740.04527.8327362999.1
2.74-30.04528.2300159398.2
3-3.360.04329.9275353798
3.36-3.870.0430.7241147298.3
3.87-4.750.03829.2178538594.4
4.75-6.710.04128.2128129091.8
6.71-25.5930.03625.548113271.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.5→25.593 Å / Cor.coef. Fo:Fc: 0.9632 / Cor.coef. Fo:Fc free: 0.9639 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. HOWEVER, THE SE-MET SIDE-CHAIN IS DISORDERED. 2. ATOM RECORD CONTAINS SUM OF TLS AND ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. HOWEVER, THE SE-MET SIDE-CHAIN IS DISORDERED. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. SULFATE MODELED IS PRESENT IN CRYSTALLIZATION CONDITIONS. 4. MAD RESTRAINTS (HL COEFFICIENTS) WERE USED DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 732 5.02 %RANDOM
Rwork0.1855 ---
obs0.1866 14577 97.34 %-
Displacement parametersBiso max: 103.62 Å2 / Biso mean: 35.7715 Å2 / Biso min: 13.39 Å2
Baniso -1Baniso -2Baniso -3
1-2.3587 Å20 Å21.1524 Å2
2--0.3584 Å20 Å2
3----2.7171 Å2
Refine analyzeLuzzati coordinate error obs: 0.253 Å
Refinement stepCycle: LAST / Resolution: 1.5→25.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms774 0 10 72 856
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d415SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes19HARMONIC2
X-RAY DIFFRACTIONt_gen_planes139HARMONIC5
X-RAY DIFFRACTIONt_it864HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion105SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1069SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d864HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1183HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.89
X-RAY DIFFRACTIONt_other_torsion2.55
LS refinement shellResolution: 1.5→1.62 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2252 162 5.51 %
Rwork0.2019 2776 -
all0.2032 2938 -
obs--97.34 %
Refinement TLS params.Method: refined / Origin x: 11.3201 Å / Origin y: 37.489 Å / Origin z: 9.0441 Å
111213212223313233
T-0.0833 Å2-0.0239 Å20.0154 Å2--0.106 Å2-0.0143 Å2---0.1116 Å2
L8.8869 °2-0.156 °22.8435 °2-3.111 °21.0697 °2--4.5473 °2
S0.1538 Å °0.0311 Å °-0.355 Å °-0.0246 Å °0.0077 Å °-0.2096 Å °0.1212 Å °-0.1994 Å °-0.1615 Å °
Refinement TLS groupSelection details: chain A

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