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- PDB-7ctx: Crystal structure of Arabidopsis thaliana SOBIR1 kinase domain(re... -

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Entry
Database: PDB / ID: 7ctx
TitleCrystal structure of Arabidopsis thaliana SOBIR1 kinase domain(residues 388-401 deleted) in complex with AMP-PNP and magnesium
ComponentsLeucine-rich repeat receptor-like serine/threonine/tyrosine-protein kinase SOBIR1
KeywordsPLANT PROTEIN / Arabidopsis thaliana / Receptor-like kinase / Autophosphorylation / Src-like inactive conformation
Function / homology
Function and homology information


negative regulation of floral organ abscission / positive regulation of defense response / defense response / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity ...negative regulation of floral organ abscission / positive regulation of defense response / defense response / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peroxisome / protein tyrosine kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
: / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...: / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Leucine-rich repeat receptor-like serine/threonine/tyrosine-protein kinase SOBIR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.907 Å
AuthorsWei, X. / Wang, Y.L. / Gu, T.Y. / Xin, F.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31571963 China
CitationJournal: To Be Published
Title: Crystal structure of Arabidopsis thaliana SOBIR1 kinase domain(residues 388-401 deleted) in complex with AMP-PNP and magnesium
Authors: Wei, X. / Wang, Y.L. / Gu, T.Y. / Xin, F.J.
History
DepositionAug 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine-rich repeat receptor-like serine/threonine/tyrosine-protein kinase SOBIR1
B: Leucine-rich repeat receptor-like serine/threonine/tyrosine-protein kinase SOBIR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6106
Polymers72,5492
Non-polymers1,0614
Water00
1
A: Leucine-rich repeat receptor-like serine/threonine/tyrosine-protein kinase SOBIR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8053
Polymers36,2751
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area13460 Å2
MethodPISA
2
B: Leucine-rich repeat receptor-like serine/threonine/tyrosine-protein kinase SOBIR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8053
Polymers36,2751
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.389, 50.732, 93.066
Angle α, β, γ (deg.)90.000, 106.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Leucine-rich repeat receptor-like serine/threonine/tyrosine-protein kinase SOBIR1 / Protein EVERSHED / Protein SUPPRESSOR OF BIR1-1


Mass: 36274.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SOBIR1, EVR, At2g31880, F20M17.8 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9SKB2, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Hepes (pH 7.0), 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 14273 / % possible obs: 98.1 % / Redundancy: 5 % / Biso Wilson estimate: 57.6 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.046 / Rrim(I) all: 0.107 / Rsym value: 0.097 / Χ2: 0.771 / Net I/av σ(I): 14.6 / Net I/σ(I): 14.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1371 / CC1/2: 0.823 / CC star: 0.95 / Rpim(I) all: 0.236 / Rrim(I) all: 0.525 / Rsym value: 0.465 / Χ2: 0.616 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CTV

7ctv


Resolution: 2.907→28.629 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2435 723 5.07 %
Rwork0.225 13534 -
obs0.2259 14257 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.39 Å2 / Biso mean: 60.1307 Å2 / Biso min: 30.49 Å2
Refinement stepCycle: final / Resolution: 2.907→28.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4534 0 2 0 4536
Biso mean--64.21 --
Num. residues----594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034696
X-RAY DIFFRACTIONf_angle_d0.5416398
X-RAY DIFFRACTIONf_chiral_restr0.043744
X-RAY DIFFRACTIONf_plane_restr0.004810
X-RAY DIFFRACTIONf_dihedral_angle_d16.2252810
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.907-3.1310.33491410.3009261596
3.131-3.44560.30761520.2657267798
3.4456-3.94310.24351390.2287271399
3.9431-4.96370.2161580.1884272899
4.9637-28.6290.20931330.215280198
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.37811.16550.17182.04551.49073.9770.1136-0.63160.09510.55020.05830.25930.73660.247-0.16730.60880.0012-0.00780.54230.00240.387-47.8912-15.767136.0285
29.4891-0.9028-1.08224.2415-1.01422.6589-0.1966-0.6562-0.0278-0.1310.3525-0.36150.46320.1247-0.23590.3801-0.0241-0.00610.2956-0.06320.3193-48.4445-14.701230.6982
31.57490.9448-0.01343.8975-2.18493.6021-0.0220.4258-0.17870.0622-0.2011-0.64280.07260.35130.19440.57350.0041-0.08850.6975-0.05860.4039-38.7697-6.675129.2604
41.74430.633-0.08611.9083-1.19863.21580.2174-0.2743-0.03490.0266-0.1453-0.00710.163-0.2072-0.04430.3858-0.02250.02150.3665-0.0230.4378-49.486-2.654117.227
50.66990.2356-0.32093.7804-0.80940.66570.0912-0.1213-0.1970.0724-0.2408-0.18540.24360.2360.13920.39960.06540.01080.39730.02580.3052-39.252-9.13119.6717
61.49950.15820.49962.7351-2.6842.9224-0.1597-0.1855-0.0837-0.60770.2201-0.460.2903-0.5019-0.0280.6394-0.0045-0.05430.409-0.0940.5218-49.9123-5.4235-6.216
71.7255-0.2545-1.03372.83370.23672.62190.11740.0762-0.3008-0.1627-0.14250.19-0.3203-0.15310.04470.48980.0089-0.09010.36030.00270.4512-46.54755.90622.4729
81.9713-2.6232-0.8554.16421.45820.73780.51960.74-0.121-0.7699-0.54710.1407-0.2988-0.26540.02480.53880.03510.00020.848-0.01660.4868-72.6733-38.47577.5495
96.2377-2.34091.62133.51632.40773.8641-0.4008-0.4996-0.3171-0.03250.26380.2426-0.42180.61130.11160.64110.01830.04940.579-0.08840.52-65.2079-39.19814.8666
104.6121-2.06022.80233.4217-0.4743.1552-0.2230.1401-0.9542-0.59540.21840.6521-0.2318-0.872-0.00630.47390.11170.04490.8101-0.08970.6872-83.9933-37.891116.7608
114.36940.03421.86322.17881.37225.94090.13410.7412-0.2218-0.1439-0.13260.04910.06790.61470.00250.35030.02750.01250.35910.03650.4152-69.7475-31.800323.6819
122.44960.7925-0.8252.12830.08382.24320.0140.0290.2012-0.1066-0.12240.0879-0.0075-0.19920.07290.33630.0051-0.01180.3556-0.01830.3726-79.0555-29.12732.6701
132.46770.091.02712.52730.57582.75680.032-0.5748-0.12780.5895-0.0272-0.1258-0.0453-0.1762-0.00510.48630.0018-0.0030.52460.05820.4677-71.0854-25.859549.7472
145.87891.2291-1.28245.8433-1.65045.01310.5045-0.26810.83610.6841-0.44980.3365-1.122-0.0767-0.03810.5085-0.0446-0.00160.3167-0.03590.3461-82.6317-17.678639.71
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 324 through 360 )A324 - 360
2X-RAY DIFFRACTION2chain 'A' and (resid 361 through 400 )A361 - 400
3X-RAY DIFFRACTION3chain 'A' and (resid 401 through 430 )A401 - 430
4X-RAY DIFFRACTION4chain 'A' and (resid 431 through 502 )A431 - 502
5X-RAY DIFFRACTION5chain 'A' and (resid 503 through 561 )A503 - 561
6X-RAY DIFFRACTION6chain 'A' and (resid 562 through 594 )A562 - 594
7X-RAY DIFFRACTION7chain 'A' and (resid 595 through 639 )A595 - 639
8X-RAY DIFFRACTION8chain 'B' and (resid 324 through 349 )B324 - 349
9X-RAY DIFFRACTION9chain 'B' and (resid 350 through 372 )B350 - 372
10X-RAY DIFFRACTION10chain 'B' and (resid 373 through 412 )B373 - 412
11X-RAY DIFFRACTION11chain 'B' and (resid 413 through 459 )B413 - 459
12X-RAY DIFFRACTION12chain 'B' and (resid 460 through 561 )B460 - 561
13X-RAY DIFFRACTION13chain 'B' and (resid 562 through 619 )B562 - 619
14X-RAY DIFFRACTION14chain 'B' and (resid 620 through 639 )B620 - 639

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