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- PDB-1nzv: Crystal Structure of Src SH2 domain bound to doubly phosphorylate... -

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Basic information

Entry
Database: PDB / ID: 1nzv
TitleCrystal Structure of Src SH2 domain bound to doubly phosphorylated peptide PQpYIpYVPA
Components
  • Doubly phosphorylated peptide PQpYIpYVPA
  • Tyrosine-protein kinase transforming protein SRC
KeywordsTRANSFERASE / SH2 domain / phosphotyrosine
Function / homology
Function and homology information


non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / histone H2AXY142 kinase activity / histone H3Y41 kinase activity / ATP binding
Similarity search - Function
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 ...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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Tyrosine-protein kinase transforming protein Src
Similarity search - Component
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLubman, O.Y. / Waksman, G.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structural and Thermodynamic Basis for the Interaction of the Src SH2 domain with the Activated form of the PDGF beta-receptor
Authors: Lubman, O.Y. / Waksman, G.
History
DepositionFeb 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 30, 2014Group: Data collection
Revision 1.4Aug 16, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN The C8 and O5 atoms of the het hroup PG4 were not modelled and are not present in the coordinates.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase transforming protein SRC
B: Tyrosine-protein kinase transforming protein SRC
C: Doubly phosphorylated peptide PQpYIpYVPA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0606
Polymers24,7953
Non-polymers2653
Water2,396133
1
A: Tyrosine-protein kinase transforming protein SRC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1074
Polymers11,8421
Non-polymers2653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein kinase transforming protein SRC
C: Doubly phosphorylated peptide PQpYIpYVPA


Theoretical massNumber of molelcules
Total (without water)12,9522
Polymers12,9522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-10 kcal/mol
Surface area6140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.256, 67.727, 29.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Tyrosine-protein kinase transforming protein SRC / p60-SRC


Mass: 11842.352 Da / Num. of mol.: 2 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus (strain Schmidt-Ruppin)
Genus: Alpharetrovirus / Species: Rous sarcoma virus / Strain: Schmidt-Ruppin / Gene: V-SRC / Plasmid: pET3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00524, EC: 2.7.1.112
#2: Protein/peptide Doubly phosphorylated peptide PQpYIpYVPA


Mass: 1110.046 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, magnesium chloride,Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
160 mg/mlprotein1drop
234 %PEG40001reservoir
30.1 MHEPES1reservoirpH8.0
40.2 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 14206 / % possible obs: 90.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 4.1 Å2 / Rsym value: 0.101
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / Num. obs: 14205 / Num. measured all: 162554 / Rmerge(I) obs: 0.104
Reflection shell
*PLUS
Highest resolution: 2.04 Å / Lowest resolution: 2.13 Å / % possible obs: 80.4 % / Rmerge(I) obs: 0.34

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1sps

1sps


Resolution: 2.1→29.64 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1128 10.4 %RANDOM
Rwork0.224 ---
all-11148 --
obs-10857 87.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.1681 Å2 / ksol: 0.368518 e/Å3
Displacement parametersBiso mean: 16.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.46 Å20 Å20 Å2
2--1.16 Å20 Å2
3---1.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 13 133 1821
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it1.662
X-RAY DIFFRACTIONc_scangle_it2.362.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 146 9.1 %
Rwork0.261 1459 -
obs--79.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_PTYR_PTR3.PARAMPROTEIN_PTYR_PTR.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4PEG.PARAMPEG_MOD1.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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