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- PDB-1rhf: Crystal Structure of human Tyro3-D1D2 -

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Basic information

Entry
Database: PDB / ID: 1rhf
TitleCrystal Structure of human Tyro3-D1D2
ComponentsTyrosine-protein kinase receptor TYRO3
KeywordsTRANSFERASE / AXL/TYRO3 FAMILY / CELLULAR ADHESION / LIGAND-INDEPENDENT DIMERIZATION / MUTATIONAL ANALYSIS
Function / homology
Function and homology information


forebrain cell migration / : / negative regulation of lymphocyte activation / natural killer cell differentiation / negative regulation of toll-like receptor signaling pathway / multicellular organism development / secretion by cell / positive regulation of viral life cycle / positive regulation of kinase activity / apoptotic cell clearance ...forebrain cell migration / : / negative regulation of lymphocyte activation / natural killer cell differentiation / negative regulation of toll-like receptor signaling pathway / multicellular organism development / secretion by cell / positive regulation of viral life cycle / positive regulation of kinase activity / apoptotic cell clearance / ovulation cycle / plasma membrane => GO:0005886 / vagina development / neuropeptide signaling pathway / phosphatidylinositol 3-kinase binding / phagocytosis / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of innate immune response / transmembrane receptor protein tyrosine kinase activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / substrate adhesion-dependent cell spreading / receptor protein-tyrosine kinase / platelet activation / platelet aggregation / negative regulation of inflammatory response / neuron cellular homeostasis / cell migration / nuclear envelope / virus receptor activity / nervous system development / spermatogenesis / protein tyrosine kinase activity / negative regulation of neuron apoptotic process / protein autophosphorylation / receptor complex / cell adhesion / endoplasmic reticulum membrane / cell surface / signal transduction / ATP binding / nucleus
Similarity search - Function
Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain ...Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / 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 / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Tyrosine-protein kinase receptor TYRO3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.96 Å
AuthorsHeiring, C. / Dahlback, B. / Muller, Y.A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Ligand recognition and homophilic interactions in Tyro3: structural insights into the Axl/Tyro3 receptor tyrosine kinase family.
Authors: Heiring, C. / Dahlback, B. / Muller, Y.A.
History
DepositionNov 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase receptor TYRO3
B: Tyrosine-protein kinase receptor TYRO3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0628
Polymers39,5222
Non-polymers5406
Water4,954275
1
A: Tyrosine-protein kinase receptor TYRO3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0045
Polymers19,7611
Non-polymers2434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Tyrosine-protein kinase receptor TYRO3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0583
Polymers19,7611
Non-polymers2972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)109.550, 109.550, 62.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Tyrosine-protein kinase receptor TYRO3 / Tyrosine-protein kinase RSE / Tyrosine-protein kinase SKY / Tyrosine-protein kinase DTK / Protein- ...Tyrosine-protein kinase RSE / Tyrosine-protein kinase SKY / Tyrosine-protein kinase DTK / Protein-tyrosine kinase byk


Mass: 19761.092 Da / Num. of mol.: 2 / Fragment: N-terminal Ig-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TYRO3, RSE, SKY, DTK, BYK / Plasmid: pET21a+ / Production host: Escherichia coli (E. coli) / References: UniProt: Q06418, EC: 2.7.1.112
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.74 Å3/Da / Density % sol: 55.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: HEPES, sodium cacodylate, magnesium acetate, PEG2000, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117 mg/mlprotein1drop
220 mMHEPES1droppH7.0
3100 mMsodium cacodylate1droppH5.4-5.7
410-14 %PEG20001drop
5200 mMmagnesium acetate1drop
64 mMdithiothreitol1drop
7100 mMsodium cacodylate1reservoirpH5.5
812 %PEG20001reservoir
9200 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 0.9766, 0.9762, 0.9252
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 7, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97661
30.97621
40.92521
ReflectionResolution: 1.95→100 Å / Num. obs: 30568 / % possible obs: 97.8 % / Rsym value: 0.043
Reflection shellResolution: 1.95→2.02 Å / Rsym value: 0.277 / % possible all: 82.9
Reflection
*PLUS
% possible obs: 0.043 % / Num. measured all: 150721
Reflection shell
*PLUS
% possible obs: 82.9 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.96→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.586 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25635 2775 9.1 %RANDOM
Rwork0.20855 ---
obs0.21286 27788 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.269 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-0.69 Å20 Å2
2---1.38 Å20 Å2
3---2.07 Å2
Refinement stepCycle: LAST / Resolution: 1.96→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2682 0 32 275 2989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212841
X-RAY DIFFRACTIONr_bond_other_d0.0020.022525
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.953901
X-RAY DIFFRACTIONr_angle_other_deg0.82935937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8145356
X-RAY DIFFRACTIONr_chiral_restr0.0860.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023142
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02506
X-RAY DIFFRACTIONr_nbd_refined0.1790.2411
X-RAY DIFFRACTIONr_nbd_other0.2450.22849
X-RAY DIFFRACTIONr_nbtor_other0.0830.21729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2178
X-RAY DIFFRACTIONr_metal_ion_refined0.1880.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.2114
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3110.237
X-RAY DIFFRACTIONr_mcbond_it1.3121.51797
X-RAY DIFFRACTIONr_mcangle_it2.26422935
X-RAY DIFFRACTIONr_scbond_it3.05331044
X-RAY DIFFRACTIONr_scangle_it4.824.5962
LS refinement shellResolution: 1.96→2.025 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.329 185
Rwork0.277 2599
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 22788 / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.402

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