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- PDB-8zkd: The Crystal Structure of the RON from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8zkd
TitleThe Crystal Structure of the RON from Biortus.
ComponentsMacrophage-stimulating protein receptor beta chain
KeywordsTRANSFERASE / Kinase / Receptor
Function / homology
Function and homology information


Signaling by MST1 / macrophage colony-stimulating factor receptor activity / hepatocyte growth factor receptor activity / pancreas development / vacuole / single fertilization / phagocytosis / stress fiber / transmembrane receptor protein tyrosine kinase activity / basal plasma membrane ...Signaling by MST1 / macrophage colony-stimulating factor receptor activity / hepatocyte growth factor receptor activity / pancreas development / vacuole / single fertilization / phagocytosis / stress fiber / transmembrane receptor protein tyrosine kinase activity / basal plasma membrane / liver development / positive regulation of MAP kinase activity / response to virus / neuron differentiation / receptor protein-tyrosine kinase / defense response / cell migration / nervous system development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / phosphorylation / innate immune response / positive regulation of cell population proliferation / enzyme binding / cell surface / signal transduction / ATP binding / plasma membrane
Similarity search - Function
RON, Sema domain / Tyrosine-protein kinase, HGF/MSP receptor / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain ...RON, Sema domain / Tyrosine-protein kinase, HGF/MSP receptor / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Immunoglobulin E-set / 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 / WD40/YVTN repeat-like-containing domain superfamily / 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
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Macrophage-stimulating protein receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Pan, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of the RON from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Pan, W.
History
DepositionMay 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage-stimulating protein receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9035
Polymers34,2481
Non-polymers6554
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-11 kcal/mol
Surface area14220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.193, 98.193, 46.873
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Macrophage-stimulating protein receptor beta chain


Mass: 34248.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MST1R, PTK8, RON / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q04912
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#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.: 192 / 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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.952998 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.952998 Å / Relative weight: 1
ReflectionResolution: 2.05→49.1 Å / Num. obs: 28370 / % possible obs: 100 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.2
Reflection shellResolution: 2.05→2.11 Å / Rmerge(I) obs: 0.769 / Num. unique obs: 2163

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→49.1 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.873 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.149 / ESU R Free: 0.151
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2305 1457 5.14 %
Rwork0.1774 26891 -
all0.18 --
obs-28348 99.972 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 54.292 Å2
Baniso -1Baniso -2Baniso -3
1--4.085 Å20 Å20 Å2
2---4.085 Å20 Å2
3---8.171 Å2
Refinement stepCycle: LAST / Resolution: 2.05→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 40 192 2643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122526
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162387
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.8473428
X-RAY DIFFRACTIONr_angle_other_deg0.4771.7585474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.355299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.019524
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.01251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.410419
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.03310123
X-RAY DIFFRACTIONr_chiral_restr0.0670.2378
X-RAY DIFFRACTIONr_chiral_restr_other0.0420.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022979
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02606
X-RAY DIFFRACTIONr_nbd_refined0.2150.2508
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22202
X-RAY DIFFRACTIONr_nbtor_refined0.180.21221
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21239
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2156
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.28
X-RAY DIFFRACTIONr_nbd_other0.1910.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2680.24
X-RAY DIFFRACTIONr_mcbond_it3.5255.5351193
X-RAY DIFFRACTIONr_mcbond_other3.5165.5341193
X-RAY DIFFRACTIONr_mcangle_it5.1469.9431490
X-RAY DIFFRACTIONr_mcangle_other5.1459.9441491
X-RAY DIFFRACTIONr_scbond_it4.4656.0661333
X-RAY DIFFRACTIONr_scbond_other4.4656.0691333
X-RAY DIFFRACTIONr_scangle_it6.90910.9071937
X-RAY DIFFRACTIONr_scangle_other6.90710.9081938
X-RAY DIFFRACTIONr_lrange_it8.98955.0812842
X-RAY DIFFRACTIONr_lrange_other8.95354.5332804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.1030.2981120.321953X-RAY DIFFRACTION100
2.103-2.1610.2911100.2961902X-RAY DIFFRACTION100
2.161-2.2230.3261020.2931903X-RAY DIFFRACTION99.9501
2.223-2.2920.2951070.2511782X-RAY DIFFRACTION99.9471
2.292-2.3670.3051060.2211752X-RAY DIFFRACTION100
2.367-2.4490.245890.2121690X-RAY DIFFRACTION100
2.449-2.5420.269990.21638X-RAY DIFFRACTION100
2.542-2.6450.227750.181598X-RAY DIFFRACTION100
2.645-2.7620.215520.1761556X-RAY DIFFRACTION100
2.762-2.8970.28620.1871482X-RAY DIFFRACTION100
2.897-3.0530.244790.1851389X-RAY DIFFRACTION100
3.053-3.2370.214820.1821303X-RAY DIFFRACTION100
3.237-3.460.231770.191212X-RAY DIFFRACTION100
3.46-3.7350.249610.191167X-RAY DIFFRACTION100
3.735-4.090.264700.1671058X-RAY DIFFRACTION100
4.09-4.5680.19370.139988X-RAY DIFFRACTION100
4.568-5.2670.167340.12866X-RAY DIFFRACTION100
5.267-6.4330.208540.154729X-RAY DIFFRACTION100
6.433-9.0210.137290.141585X-RAY DIFFRACTION100
9.021-49.10.209200.157338X-RAY DIFFRACTION98.895

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