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- PDB-7ctv: Crystal structure of Arabidopsis thaliana SOBIR1 kinase domain D4... -

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Basic information

Entry
Database: PDB / ID: 7ctv
TitleCrystal structure of Arabidopsis thaliana SOBIR1 kinase domain D489A mutant 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 / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / defense response / peroxisome / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity ...negative regulation of floral organ abscission / positive regulation of defense response / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / defense response / peroxisome / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / phosphorylation / 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 / Protein kinase domain profile. ...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: 2.88561127202 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 D489A mutant 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

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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)76,6306
Polymers75,5692
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)38,3153
Polymers37,7851
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area14190 Å2
MethodPISA
2
B: Leucine-rich repeat receptor-like serine/threonine/tyrosine-protein kinase SOBIR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3153
Polymers37,7851
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.570, 50.889, 105.416
Angle α, β, γ (deg.)90.000, 95.348, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 37784.508 Da / Num. of mol.: 2 / Mutation: D489A
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: 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
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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.15
Details: 0.1 M Bistris propane (pH 8.15), 18% PEG8000, 3% MPD, 8% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 16161 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 83.7 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.041 / Rrim(I) all: 0.104 / Rsym value: 0.095 / Χ2: 0.946 / Net I/av σ(I): 19.9 / Net I/σ(I): 19.9
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1595 / CC1/2: 0.854 / CC star: 0.96 / Rpim(I) all: 0.233 / Rrim(I) all: 0.548 / Rsym value: 0.494 / Χ2: 0.651 / % possible all: 99.1

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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: 5LPY

5lpy


Resolution: 2.88561127202→43.3859785821 Å / SU ML: 0.312397617249 / Cross valid method: FREE R-VALUE / σ(F): 1.36130822499 / Phase error: 27.8906994263
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239387336707 774 4.79494486433 %
Rwork0.21700830008 15368 -
obs0.218126395507 16142 98.247108947 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.2935964329 Å2
Refinement stepCycle: LAST / Resolution: 2.88561127202→43.3859785821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4505 0 2 0 4507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002040981139744597
X-RAY DIFFRACTIONf_angle_d0.4928616789896265
X-RAY DIFFRACTIONf_chiral_restr0.0412680248858733
X-RAY DIFFRACTIONf_plane_restr0.00413267640944795
X-RAY DIFFRACTIONf_dihedral_angle_d17.14085600862737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.886-3.06640.3138843867581010.2859705223992358X-RAY DIFFRACTION90.1392961877
3.0664-3.3030.3079581138341330.2676288978522557X-RAY DIFFRACTION99.9628390933
3.303-3.63530.2778458770281380.2478022276382596X-RAY DIFFRACTION100
3.6353-4.1610.2504155355971280.2180872378712584X-RAY DIFFRACTION100
4.161-5.24090.2268912399271370.2006324341942604X-RAY DIFFRACTION100
5.2409-43.380.2111053653991370.1986334509942669X-RAY DIFFRACTION99.3626062323
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)
14.449120866474.749966114581.734273451738.35284682062.562950186352.45164198036-0.1085268368221.590844853880.181781981224-0.5506061384591.36430564663-1.56327047650.6861388702230.145310541768-0.8484605280191.157460365110.1303074913080.0177751919561.15359352269-0.3516018256010.58856649960429.0336340178-10.096241593630.8568767626
24.463524765190.7576031698833.314137571522.452369026052.45920504067.392203421460.06609720078210.688019999798-0.667011008019-0.6155336357090.424743927037-0.446825401836-0.0900050230861-0.496040279036-0.2176826463950.5081039698590.2100856996980.04350898927760.8994014473220.05192438318571.2911441793727.9608257679-16.413404493343.2894881776
33.664093160061.683290621014.037468841196.747666997670.3941571951334.735660168430.5012340132730.111306489006-0.784826814074-0.3160108954260.0512918152399-0.08899100519220.51922539835-0.401142512106-0.1738273489090.4665068613190.02209658070490.06694435851390.774603786681-0.03813906361640.47670799054316.5634219697-10.873309835633.6143975896
42.44869076686-2.91556812584-0.6042267471345.767086641972.684858040135.798928224170.2248180321370.00502105528484-0.229717499821-1.106231384960.2458059279710.1684269057290.134848170524-0.672171040995-0.3017148270070.693191743415-0.2074064994270.1547002920460.7964752412930.09550142925210.73922684175919.5877559179-3.1430704312236.0795616896
52.692656360331.586463666661.360815588853.727373464722.552357757556.516651113710.0872594401018-0.239354779165-0.3856412246150.3851391189650.515293910884-0.5470668842711.098196929880.505258967519-0.5944606936050.4206624572260.07545614400720.02780667790430.5570665629390.09923413850750.80940922731521.7192518714-6.3118477810753.101885669
64.91021799291.451310745321.962189355743.73465474241.992320572263.058253692610.00931799531350.439580636820.18622516846-0.341117394826-0.1249174549560.0417056219204-0.1562354685440.1730559352850.1711580767250.3302314617610.09290778199170.04020619712230.5029900405390.08068669826450.532840336818.09079246505-2.8250881660447.2818229313
79.71811261701-3.34128014062-0.001374487371985.793190937542.880063139046.22085605543-0.109250662816-0.917192610104-0.3718468239051.16366959860.1316724771650.635680403050.4255514255220.05324931003640.05711710460270.4725009427620.04089091570340.1107323494590.5402834137880.03170164010390.5780069293083.999148265610.89176675164165.5718957909
87.3892007823-0.1711573071920.6185575188975.556050563811.868961162584.6949501640.0652754253076-0.3428781630671.27511041788-0.548240307402-0.4610819928010.0392539137909-0.7988138416190.1884546556610.2059237226420.5723645373180.00361617441125-0.02466592811740.3170914214820.06699082214440.5699916063930.5898624932598.6686767022950.404974621
99.31121126353-1.119490472290.966710708512.11121046138-1.308153752442.575773970480.288116497558-1.37829017846-2.245853647660.7734598704080.39664503216-0.06080768092792.151107631831.073923857-0.2806483581111.325571866450.7464139344410.05870895771161.09504670977-0.2513083436070.16035521697118.9689711225-12.890343503176.7008323552
102.683604930731.17598732997-1.319088056652.956736679251.431068953812.62921258517-0.596774690929-1.88053719335-1.414069828271.5822157354-0.0528220778401-0.6682940586761.446464114971.649318348780.2547020155421.153137197610.4514513498710.2900482556641.497565471410.4122203590730.84946665734617.6721085931-14.834273281988.4557202829
115.45163624374-0.1356272434380.9801787174713.071349726444.744512252279.814773354190.573969071786-0.639213318856-1.30913847311-0.442954043692-0.684231425251-0.02397659090180.429105744203-0.776418093171-0.03641869956270.9535106910260.02331908875340.002134291772621.075422795660.2018545125240.7520476549817.79866670214-7.6862806610781.6273445833
126.075482411311.02325480353-2.927778458012.7412971651-1.001347920491.551321858350.596805130578-0.735182499071-0.7913458106891.70941692309-1.08560938527-0.8650772934610.322761753561-0.136483415576-0.3902818429631.07640733639-0.156549957485-0.1506734379161.144954663670.1064114867950.70181354968217.9564001013-5.03052967117104.210657514
136.447410866752.21730503385-0.3099140392274.983905704392.845452187523.23301580831-0.1764341554040.4958582758791.70154614996-0.0428964586970.1677571662980.775297317447-0.6699157416930.789658766617-0.2172919527810.900323221062-0.0918156261479-0.08729691210170.9162062706020.2201200408020.5829447577966.666631361782.7280581983694.7409404968
145.878888524431.12548879260.7129438903524.351785320692.115561143321.03594426799-0.1995202140811.028259968680.4709978287520.58210568918-0.112614585050.06029936515310.379240018687-0.1162554381960.2215101389191.089665618720.01359316287380.02439405575610.9366230438640.0327949036340.683541139806-4.28513722261-12.441146649496.4120329175
156.629023755190.793088464141.285354010451.533418451421.291832331838.178369750740.218432933522-0.181564431194-0.6545402593430.335052590197-0.448624688398-0.4897932910431.864327592720.0779680643244-0.1226547095141.11862933161-0.01857467806980.06615376373730.588549941354-0.05856372893280.5184657720940.723753717694-5.20424550794109.257981492
165.811109891720.877096596124-4.628265784993.72820457088-1.316437341063.808880588480.761383861487-0.6288322400470.9666981199211.17925329166-0.3300563814990.2519395059510.1498090656560.458539116401-0.3094712722811.183653166790.0542258364985-0.1678269680370.833603241336-0.01015650649370.5351296320822.336428558894.71386612977115.312625573
176.284157042060.6592274602993.664270030570.03649178916980.4082994562062.552766884840.262141093165-0.5434087717041.00812461359-0.0878405187-0.444067058966-0.08064401708640.303002157950.3106872755160.1636060907741.133670798020.0882154099080.070858376850.668100858131-0.08468935406740.681001332839-4.296839399098.60208913199101.4952938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 324 through 342 )
2X-RAY DIFFRACTION2chain 'A' and (resid 343 through 371 )
3X-RAY DIFFRACTION3chain 'A' and (resid 372 through 412 )
4X-RAY DIFFRACTION4chain 'A' and (resid 413 through 430 )
5X-RAY DIFFRACTION5chain 'A' and (resid 431 through 459 )
6X-RAY DIFFRACTION6chain 'A' and (resid 460 through 561 )
7X-RAY DIFFRACTION7chain 'A' and (resid 562 through 619 )
8X-RAY DIFFRACTION8chain 'A' and (resid 620 through 639 )
9X-RAY DIFFRACTION9chain 'B' and (resid 325 through 347 )
10X-RAY DIFFRACTION10chain 'B' and (resid 348 through 398 )
11X-RAY DIFFRACTION11chain 'B' and (resid 399 through 437 )
12X-RAY DIFFRACTION12chain 'B' and (resid 438 through 459 )
13X-RAY DIFFRACTION13chain 'B' and (resid 460 through 505 )
14X-RAY DIFFRACTION14chain 'B' and (resid 506 through 544 )
15X-RAY DIFFRACTION15chain 'B' and (resid 545 through 577 )
16X-RAY DIFFRACTION16chain 'B' and (resid 578 through 619 )
17X-RAY DIFFRACTION17chain 'B' and (resid 620 through 640 )

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