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- PDB-4q3i: Structure of the OsSERK2 leucine rich repeat extracellular domain -

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Basic information

Entry
Database: PDB / ID: 4q3i
TitleStructure of the OsSERK2 leucine rich repeat extracellular domain
ComponentsOsSERK2 D128N
KeywordsTRANSFERASE / Leucine Rich Repete / toll-like receptor / brassinosteroids
Function / homology
Function and homology information


protein kinase activity / phosphorylation / ATP binding / membrane
Similarity search - Function
Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Protein tyrosine and serine/threonine kinase ...Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 / Alpha Beta
Similarity search - Domain/homology
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsMcAndrew, R.P. / Pruitt, R.N. / Kamita, S.G. / Pereira, J.H. / Majumder, D. / Hammock, B.D. / Adams, P.D. / Ronald, P.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the OsSERK2 leucine-rich repeat extracellular domain.
Authors: McAndrew, R. / Pruitt, R.N. / Kamita, S.G. / Pereira, J.H. / Majumdar, D. / Hammock, B.D. / Adams, P.D. / Ronald, P.C.
History
DepositionApr 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Jul 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_leaving_atom_flag / _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: OsSERK2 D128N
B: OsSERK2 D128N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9564
Polymers54,5132
Non-polymers4422
Water1,982110
1
A: OsSERK2 D128N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4782
Polymers27,2571
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OsSERK2 D128N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4782
Polymers27,2571
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.881, 50.646, 83.161
Angle α, β, γ (deg.)90.00, 113.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein OsSERK2 D128N


Mass: 27256.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / References: UniProt: Q01JP8*PLUS
#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.: 2
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.: 110 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Bis-Tris pH 6.5, 200 mM MgCl2, and 23% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2013
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 23648 / Num. obs: 22466 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.35→2.39 Å / % possible all: 71.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.phaser: dev_1525)model building
PHENIX(phenix.refine: dev_1616)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXdev_1525phasing
RefinementResolution: 2.35→42.215 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 32.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2858 1757 9.92 %
Rwork0.2362 --
obs0.2411 17720 78.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→42.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 0 28 110 3560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023526
X-RAY DIFFRACTIONf_angle_d0.6124803
X-RAY DIFFRACTIONf_dihedral_angle_d10.6691297
X-RAY DIFFRACTIONf_chiral_restr0.024563
X-RAY DIFFRACTIONf_plane_restr0.003620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.38560.3863550.3092519X-RAY DIFFRACTION33
2.3856-2.45580.34820.268687X-RAY DIFFRACTION45
2.4558-2.5350.2992870.2806824X-RAY DIFFRACTION52
2.535-2.62560.37541030.2737938X-RAY DIFFRACTION60
2.6256-2.73080.35061220.28521081X-RAY DIFFRACTION69
2.7308-2.8550.36651370.28021238X-RAY DIFFRACTION80
2.855-3.00550.3371490.2781394X-RAY DIFFRACTION89
3.0055-3.19370.29081630.27171456X-RAY DIFFRACTION93
3.1937-3.44020.29591620.25991500X-RAY DIFFRACTION96
3.4402-3.78620.2841650.21321574X-RAY DIFFRACTION98
3.7862-4.33360.23331710.19681530X-RAY DIFFRACTION98
4.3336-5.45810.24621800.19341588X-RAY DIFFRACTION99
5.4581-42.22160.26651810.23231634X-RAY DIFFRACTION99
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)
14.049-1.30560.52313.7626-0.89771.9273-0.0429-0.1061-0.10640.24690.03160.3607-0.17610.0973-0.01510.33120.00490.15530.2508-0.05540.3082-55.447519.0021164.1306
21.6196-0.4671-2.10834.32630.84234.480.1260.27910.0655-0.164-0.0805-0.0325-0.7634-0.0884-0.06930.36090.03230.0410.26310.04170.2985-49.56718.224154.3503
32.7512-1.3522-0.84082.5232-1.63254.6047-0.3432-0.1650.05350.179-0.04140.02360.23130.11480.39370.3509-0.01230.01810.116-0.00650.3203-48.432210.0823162.493
42.90870.16580.00752.1897-0.432.1973-0.3065-0.1879-0.17910.09140.11980.06490.1003-0.0890.23310.37110.03420.07730.208-0.04120.3054-47.58171.9804163.6239
58.51332.0552-1.53484.7431-0.89336.3428-0.0470.5497-0.31720.331-0.10380.1998-0.2653-0.56060.1240.23760.0411-0.0340.1836-0.06060.2712-45.7633-1.127153.8194
61.6927-0.2240.73492.27560.41534.1767-0.0822-0.13150.02750.13380.16670.4488-0.1912-0.266-0.04340.3613-0.02280.0150.2602-0.04220.2383-42.6256-5.9931159.492
72.99440.57681.5623.8721.60523.69780.3809-0.3022-0.19270.23830.0414-0.33880.0209-0.34-0.34480.2902-0.02430.01160.2767-0.00920.1902-38.4814-9.728161.9767
80.4204-0.2536-0.54093.2618-0.71541.52870.0237-0.0915-0.0039-0.1325-0.0345-0.07860.04530.0436-0.01470.29050.0029-0.04140.2786-0.02540.2468-32.4604-12.5078159.5991
92.9363-1.15890.07954.06472.7565.24650.06840.00440.13010.44140.24570.01650.7326-0.0081-0.27140.46760.0672-0.06930.25950.01980.1793-28.074-21.2215166.1462
101.5122-0.2865-0.5723.05081.03791.2379-0.0290.0398-0.1876-0.00770.002-0.15130.0668-0.03130.03190.34340.05950.06390.2590.00030.3303-67.9263-22.0834174.2815
113.6366-0.13090.72091.73810.67681.7962-0.00910.25-0.1388-0.21030.0421-0.08410.10720.20440.010.30310.03410.01160.24810.01650.2264-72.619-6.2314180.4472
121.5031-0.12-0.04283.32830.63551.8812-0.08130.03880.2291-0.074-0.00780.0707-0.06140.01460.07470.20690.0477-0.00980.2470.01630.2523-73.40885.4767192.0662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 31:64 )A31 - 64
2X-RAY DIFFRACTION2( CHAIN A AND RESID 65:80 )A65 - 80
3X-RAY DIFFRACTION3( CHAIN A AND RESID 81:108 )A81 - 108
4X-RAY DIFFRACTION4( CHAIN A AND RESID 109:139 )A109 - 139
5X-RAY DIFFRACTION5( CHAIN A AND RESID 140:152 )A140 - 152
6X-RAY DIFFRACTION6( CHAIN A AND RESID 153:173 )A153 - 173
7X-RAY DIFFRACTION7( CHAIN A AND RESID 174:191 )A174 - 191
8X-RAY DIFFRACTION8( CHAIN A AND RESID 192:232 )A192 - 232
9X-RAY DIFFRACTION9( CHAIN A AND RESID 233:248 )A233 - 248
10X-RAY DIFFRACTION10( CHAIN B AND RESID 31:120 )B31 - 120
11X-RAY DIFFRACTION11( CHAIN B AND RESID 121:173 )B121 - 173
12X-RAY DIFFRACTION12( CHAIN B AND RESID 174:248 )B174 - 248

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