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- PDB-5jfk: Crystal structure of a TDR receptor -

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Basic information

Entry
Database: PDB / ID: 5jfk
TitleCrystal structure of a TDR receptor
ComponentsLeucine-rich repeat receptor-like protein kinase TDR
KeywordsSIGNALING PROTEIN / LRR receptor / extracellular domain / TDR / TRANSFERASE
Function / homology
Function and homology information


procambium histogenesis / xylem development / phloem or xylem histogenesis / secondary shoot formation / non-specific serine/threonine protein kinase / phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / 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, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Leucine-rich repeat receptor-like protein kinase TDR
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.647 Å
AuthorsLi, Z. / Xu, G.
CitationJournal: To Be Published
Title: Crystal structure of a TDR receptor
Authors: Li, Z. / Xu, G.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine-rich repeat receptor-like protein kinase TDR
B: Leucine-rich repeat receptor-like protein kinase TDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,07212
Polymers134,8602
Non-polymers2,21210
Water2,612145
1
A: Leucine-rich repeat receptor-like protein kinase TDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5366
Polymers67,4301
Non-polymers1,1065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leucine-rich repeat receptor-like protein kinase TDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5366
Polymers67,4301
Non-polymers1,1065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.336, 92.336, 250.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Leucine-rich repeat receptor-like protein kinase TDR / Protein PHLOEM INTERCALATED WITH XYLEM / Tracheary element differentiation inhibitory factor ...Protein PHLOEM INTERCALATED WITH XYLEM / Tracheary element differentiation inhibitory factor receptor / TDIF receptor


Mass: 67429.945 Da / Num. of mol.: 2 / Fragment: UNP residues 30-642
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TDR, PXY, At5g61480, MCI2.4
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9FII5, non-specific serine/threonine protein kinase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 4.15 Å3/Da / Density % sol: 70.36 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 200mM MgSO4, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0422 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0422 Å / Relative weight: 1
ReflectionResolution: 2.647→50 Å / Num. obs: 56517 / % possible obs: 93.1 % / Redundancy: 3.1 % / Net I/σ(I): 17.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.647→46.168 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 1645 3.08 %
Rwork0.2217 --
obs0.2226 53447 88.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.647→46.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8926 0 140 145 9211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059296
X-RAY DIFFRACTIONf_angle_d1.10212648
X-RAY DIFFRACTIONf_dihedral_angle_d13.7373308
X-RAY DIFFRACTIONf_chiral_restr0.0561448
X-RAY DIFFRACTIONf_plane_restr0.0051636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.647-2.72490.3525710.29382664X-RAY DIFFRACTION54
2.7249-2.81280.3248990.2983261X-RAY DIFFRACTION67
2.8128-2.91330.30861320.2863759X-RAY DIFFRACTION77
2.9133-3.030.31761120.27574068X-RAY DIFFRACTION83
3.03-3.16780.29351220.25694412X-RAY DIFFRACTION89
3.1678-3.33480.27241530.25714642X-RAY DIFFRACTION95
3.3348-3.54370.3181360.24234783X-RAY DIFFRACTION97
3.5437-3.81720.22311480.20034826X-RAY DIFFRACTION99
3.8172-4.20110.22611580.18484874X-RAY DIFFRACTION99
4.2011-4.80840.19931550.17794856X-RAY DIFFRACTION99
4.8084-6.05590.25181770.21274862X-RAY DIFFRACTION100
6.0559-46.1750.2421820.23874795X-RAY DIFFRACTION97
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)
10.17710.18-0.0880.2153-0.39360.6922-0.30570.31950.462-1.1765-0.3376-0.53220.64340.8454-0.01461.45470.1208-0.09920.26550.39510.786411.255922.1204-23.8192
21.7257-0.8803-0.01181.7455-1.84185.6317-0.0977-0.15360.3688-0.80950.2770.71210.2885-0.8031-0.10360.7285-0.1226-0.3390.34730.20220.7141-1.618616.1203-10.4133
32.9188-0.37340.26812.7414-0.34931.8291-0.0369-0.3725-0.1169-0.46960.31681.11560.1708-0.6988-0.25630.5103-0.0862-0.22630.55990.26190.6209-2.9705-0.3416.8632
44.24770.12761.29112.37390.63813.10090.1549-0.1662-0.5990.12270.15320.11460.4236-0.1413-0.17340.4254-0.0659-0.15010.45070.09240.453113.8001-12.19917.781
54.62721.35721.52853.14420.65444.38920.19330.1857-0.81330.08940.1567-0.51830.50310.528-0.30670.36790.043-0.11180.5221-0.07330.533535.6469-9.895425.7645
62.96491.47842.26173.38721.07684.1043-0.30580.19080.0384-0.01430.321-0.4267-0.18330.4815-0.03330.32230.0405-0.10860.6007-0.14320.461449.97647.000134.5141
73.03071.33710.17742.04932.13312.8578-0.26660.0412-0.11410.17220.3008-0.5872-0.4773-0.005-0.24210.5180.1862-0.31020.5268-0.17560.778749.424321.324344.1512
81.26320.00751.87060.2731-0.16083.3759-0.1237-0.86050.08590.0593-0.3443-0.459-0.6429-0.78520.48480.23990.1857-0.31661.26570.27520.762168.3665-35.159222.7985
91.7526-0.81112.05061.7211-0.50115.30690.1815-0.6804-0.70450.0419-0.1084-0.42990.6463-0.0685-0.07720.3657-0.0938-0.1770.71680.32250.733562.3076-47.78689.4226
102.7074-0.41240.6223.1922-0.99052.40290.454-0.3988-0.9822-0.3413-0.07040.11930.7012-0.1863-0.31470.5802-0.0936-0.25860.49630.21780.581945.8285-49.1412-7.877
112.1276-0.0689-0.82543.999-1.09483.02890.17590.1822-0.0717-0.16890.15990.51470.1545-0.5058-0.22040.4328-0.0785-0.10690.41930.15980.415333.9746-32.382-18.8375
123.13251.4266-0.23813.1888-0.95873.42930.1954-0.02340.54980.1420.09380.711-0.4615-0.4309-0.24170.51260.06080.09620.36360.10380.539236.2403-10.5299-26.7981
133.51121.2453-0.97793.1044-2.76964.24510.36540.03460.53870.2917-0.2105-0.0586-0.50350.1271-0.1130.57810.03850.15920.32840.1050.49153.17893.7607-35.5558
141.6835-0.2101-1.83171.41661.72423.62530.57230.21730.98590.0970.1527-0.8223-0.2260.7333-0.29050.62650.1850.27150.58960.38960.768567.97433.2678-44.9759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 40:100)
2X-RAY DIFFRACTION2chain A and (resseq 101:200)
3X-RAY DIFFRACTION3chain A and (resseq 201:300)
4X-RAY DIFFRACTION4chain A and (resseq 301:400)
5X-RAY DIFFRACTION5chain A and (resseq 401:500)
6X-RAY DIFFRACTION6chain A and (resseq 501:600)
7X-RAY DIFFRACTION7chain A and (resseq 601:625)
8X-RAY DIFFRACTION8chain B and (resseq 40:100)
9X-RAY DIFFRACTION9chain B and (resseq 101:200)
10X-RAY DIFFRACTION10chain B and (resseq 201:300)
11X-RAY DIFFRACTION11chain B and (resseq 301:400)
12X-RAY DIFFRACTION12chain B and (resseq 401:500)
13X-RAY DIFFRACTION13chain B and (resseq 501:600)
14X-RAY DIFFRACTION14chain B and (resseq 601:625)

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