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- PDB-6s9f: Drosophila OTK, extracellular domains 3-5 -

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Basic information

Entry
Database: PDB / ID: 6s9f
TitleDrosophila OTK, extracellular domains 3-5
ComponentsTyrosine-protein kinase-like otk
KeywordsSIGNALING PROTEIN / OTK / Off-track / Ig-like domain / signalling
Function / homology
Function and homology information


internal genitalia morphogenesis / imaginal disc-derived female genitalia morphogenesis / imaginal disc-derived male genitalia morphogenesis / photoreceptor cell axon guidance / semaphorin receptor binding / Wnt-protein binding / regulation of canonical Wnt signaling pathway / retinal ganglion cell axon guidance / cell adhesion molecule binding / transmembrane receptor protein tyrosine kinase activity ...internal genitalia morphogenesis / imaginal disc-derived female genitalia morphogenesis / imaginal disc-derived male genitalia morphogenesis / photoreceptor cell axon guidance / semaphorin receptor binding / Wnt-protein binding / regulation of canonical Wnt signaling pathway / retinal ganglion cell axon guidance / cell adhesion molecule binding / transmembrane receptor protein tyrosine kinase activity / axon guidance / negative regulation of canonical Wnt signaling pathway / cell-cell junction / membrane => GO:0016020 / cell adhesion / protein heterodimerization activity / axon / protein homodimerization activity / ATP binding / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin ...Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Tyrosine-protein kinase-like otk
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.969 Å
AuthorsRozbesky, D. / Jones, E.Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC375/A17721 United Kingdom
Medical Research Council (United Kingdom)MR/M000141/1 United Kingdom
CitationJournal: Structure / Year: 2020
Title: Drosophila OTK Is a Glycosaminoglycan-Binding Protein with High Conformational Flexibility.
Authors: Rozbesky, D. / Monistrol, J. / Jain, V. / Hillier, J. / Padilla-Parra, S. / Jones, E.Y.
History
DepositionJul 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase-like otk
B: Tyrosine-protein kinase-like otk
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,60621
Polymers126,2792
Non-polymers3,32719
Water7,746430
1
A: Tyrosine-protein kinase-like otk
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,85111
Polymers63,1401
Non-polymers1,71210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase-like otk
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,75510
Polymers63,1401
Non-polymers1,6159
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.975, 189.909, 131.906
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-768-

HOH

21A-848-

HOH

31A-916-

HOH

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Components

#1: Protein Tyrosine-protein kinase-like otk / Gp160-Dtrk / Dtrk / Off-track / Tyrosine-protein kinase-like 7 homolog


Mass: 63139.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: otk, CG8967 / Plasmid: pHLsec / Cell (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q6AWJ9
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.85 Å3/Da / Density % sol: 68.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.05 M HEPES (pH 7.0), 0.01 M magnesium chloride, 150 mM NDSB256 and 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.969→49.38 Å / Num. obs: 71214 / % possible obs: 97.29 % / Redundancy: 5.9 % / CC1/2: 1 / Rrim(I) all: 0.083 / Net I/σ(I): 11
Reflection shellResolution: 1.97→2 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6384 / CC1/2: 0.5 / Rrim(I) all: 0.835 / % possible all: 85.14

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIXdev_3488refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2iep, 2v9t, 4of6

2iep

2v9t

4of6


Resolution: 1.969→47.477 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.77
RfactorNum. reflection% reflection
Rfree0.2353 3536 5.04 %
Rwork0.2068 --
obs0.2082 70203 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.42 Å2 / Biso mean: 50.5603 Å2 / Biso min: 18.38 Å2
Refinement stepCycle: final / Resolution: 1.969→47.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4620 0 203 430 5253
Biso mean--77.3 50.98 -
Num. residues----598
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.969-1.9960.46751100.4112218580
1.996-2.02450.39391200.3932241088
2.0245-2.05470.36611250.3688244391
2.0547-2.08690.36541470.3333253594
2.0869-2.12110.34651280.3104263296
2.1211-2.15760.31231320.2853265798
2.1576-2.19690.29581340.2821268798
2.1969-2.23910.34771390.2669264698
2.2391-2.28480.33491480.2605267298
2.2848-2.33450.30741180.2503270898
2.3345-2.38880.27031440.2424267398
2.3888-2.44860.25671320.2348269399
2.4486-2.51480.28581350.2314270599
2.5148-2.58870.28181420.218269499
2.5887-2.67230.25221640.216268499
2.6723-2.76780.24881580.2112708100
2.7678-2.87860.24381520.2075272899
2.8786-3.00960.22241540.20242708100
3.0096-3.16820.20711310.1982754100
3.1682-3.36670.21581370.19052764100
3.3667-3.62650.18491440.1912735100
3.6265-3.99130.22221480.16532791100
3.9913-4.56850.18031700.15372742100
4.5685-5.75420.20671480.16322824100
5.7542-47.4770.2051760.19712889100
Refinement TLS params.Method: refined / Origin x: -38.8222 Å / Origin y: -25.6379 Å / Origin z: -2.3824 Å
111213212223313233
T0.2154 Å2-0.0031 Å2-0.0133 Å2-0.157 Å2-0.0279 Å2--0.1988 Å2
L0.3864 °2-0.0589 °20.0309 °2-0.1376 °2-0.0403 °2--0.2221 °2
S-0.0278 Å °-0.0808 Å °0.0569 Å °-0.0197 Å °0.0005 Å °-0.0284 Å °-0.0461 Å °0.0256 Å °-0.0011 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA246 - 667
2X-RAY DIFFRACTION1allB246 - 667
3X-RAY DIFFRACTION1allC1 - 7
4X-RAY DIFFRACTION1allS1 - 431

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