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- PDB-4q3g: Structure of the OsSERK2 leucine rich repeat extracellular domain -

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Basic information

Entry
Database: PDB / ID: 4q3g
TitleStructure of the OsSERK2 leucine rich repeat extracellular domain
ComponentsOsSERK2
KeywordsTRANSFERASE / Leucine rich repeat / toll-like receptors / brassinosteroid
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / membrane
Similarity search - Function
: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / : / Leucine-rich repeat region / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat ...: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / : / Leucine-rich repeat region / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.787 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
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OsSERK2
B: OsSERK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9584
Polymers54,5152
Non-polymers4422
Water27015
1
A: OsSERK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4792
Polymers27,2581
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OsSERK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4792
Polymers27,2581
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.900, 81.656, 126.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein OsSERK2


Mass: 27257.660 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-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


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


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.96 %
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: Apr 12, 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: 2.78→50 Å / Num. all: 14452 / Num. obs: 13469 / % possible obs: 93.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.78→2.8 Å / % possible all: 94.5

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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: 2.787→42.579 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 34.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2767 508 4.98 %
Rwork0.2387 --
obs0.2406 10204 75.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.787→42.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 0 28 15 3465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033526
X-RAY DIFFRACTIONf_angle_d0.9024803
X-RAY DIFFRACTIONf_dihedral_angle_d11.7161297
X-RAY DIFFRACTIONf_chiral_restr0.032563
X-RAY DIFFRACTIONf_plane_restr0.004620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7867-3.0670.3562630.28381196X-RAY DIFFRACTION38
3.067-3.51070.3371260.28322446X-RAY DIFFRACTION78
3.5107-4.42230.26761550.22352953X-RAY DIFFRACTION93
4.4223-42.58390.24721640.22483101X-RAY DIFFRACTION93
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)
13.28490.52330.71220.7877-0.38621.311-0.02390.20540.5723-0.2912-0.44510.0269-0.3434-0.04650.30980.3975-0.0887-0.13760.76870.16890.26695.510250.264362.2595
24.3263-0.93840.78883.2884-1.86542.41070.0593-0.0667-0.5307-0.87770.09090.0738-0.041-0.7212-0.20750.5665-0.1993-0.10630.7722-0.15150.2714-0.232444.573165.5512
31.4844-1.18481.15071.20010.38287.5751-0.2591-0.6397-0.08540.2846-0.41160.0166-0.81710.22610.4930.3009-0.1256-0.11270.34240.09840.55963.066650.76674.9149
41.8396-1.6420.55245.40233.58636.24070.3011-0.2017-0.22830.0894-0.70570.05880.2709-0.37140.36110.2148-0.0702-0.08920.39990.05390.161511.229543.492370.8308
54.0491.84660.28541.79290.58281.38530.05530.0172-0.3212-0.02840.0945-0.07550.1965-0.21550.03410.2563-0.2808-0.08730.52680.17540.422719.219443.080866.5417
62.7384-0.2120.46353.8831.6433.92990.31130.3130.0068-0.2192-0.277-0.5087-0.3295-0.18160.03640.1395-0.0232-0.03280.21370.0090.255423.035243.662376.0885
74.61420.0609-0.9683.9276-0.58892.4012-0.0470.0530.2488-0.64290.1565-0.04480.1195-0.0585-0.09070.2178-0.1621-0.01580.2813-0.0250.2430.837337.585179.0689
80.91290.2135-0.19660.71460.41191.0694-0.0461-0.10940.2359-0.05820.2553-0.10710.20260.01610.340.4292-0.2473-0.12920.2313-0.16830.198332.746236.185482.6208
94.15780.95910.4443.88642.0211.6431-0.2862-0.4915-0.36960.27290.04280.29630.5583-0.37910.16980.2656-0.1634-0.07040.22110.04280.308934.479735.171388.5378
100.47020.11730.60440.58030.36762.11160.165-0.3072-0.2392-0.1661-0.0482-0.02460.23640.1180.16230.61410.02-0.05740.42170.09810.070142.157827.894384.7753
110.15950.18790.24642.7469-0.16270.46320.1053-0.3226-0.26030.5045-0.3041-0.3388-0.10480.04120.35710.4169-0.19880.12610.78380.05230.322-19.174632.1693117.6129
121.8089-0.4446-0.59660.521-0.73572.09280.0034-0.10770.21010.06510.1584-0.0592-0.0193-0.71730.20.1782-0.13070.10950.5286-0.16220.1119-25.364237.0913114.4471
134.40721.63860.74361.45811.05823.45060.2501-0.12110.33330.1428-0.20280.0010.4279-0.267-0.05650.3165-0.03070.06640.252-0.03720.2204-13.697336.2412107.8713
142.1368-0.09810.95472.13851.6693.60120.1075-0.50270.0731-0.06960.00140.19640.04210.2342-0.20940.2054-0.12170.04860.3606-0.19670.1029-1.012539.4242105.6707
154.0855-0.0137-0.43130.99710.63691.11950.02370.1853-0.0180.7629-0.089-0.18480.0575-0.06670.08180.37830.00690.02380.11050.02090.20074.960339.8504100.2534
163.1217-0.1597-0.03083.82351.04052.062-0.03960.06490.2341-0.56070.1099-0.0103-0.07910.3460.0150.2193-0.1065-0.03180.31750.03860.24858.621545.724894.8267
178.3258-1.9114-2.96294.89031.25383.44710.2131-0.74170.6769-0.15120.0521-0.0845-0.21340.0025-0.1550.1598-0.0717-0.01620.3849-0.1560.39617.282753.503295.3452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 80 )
4X-RAY DIFFRACTION4chain 'A' and (resid 81 through 108 )
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 120 )
6X-RAY DIFFRACTION6chain 'A' and (resid 121 through 173 )
7X-RAY DIFFRACTION7chain 'A' and (resid 174 through 191 )
8X-RAY DIFFRACTION8chain 'A' and (resid 192 through 213 )
9X-RAY DIFFRACTION9chain 'A' and (resid 214 through 232 )
10X-RAY DIFFRACTION10chain 'A' and (resid 233 through 248 )
11X-RAY DIFFRACTION11chain 'B' and (resid 31 through 44 )
12X-RAY DIFFRACTION12chain 'B' and (resid 45 through 64 )
13X-RAY DIFFRACTION13chain 'B' and (resid 65 through 132 )
14X-RAY DIFFRACTION14chain 'B' and (resid 133 through 163 )
15X-RAY DIFFRACTION15chain 'B' and (resid 164 through 191 )
16X-RAY DIFFRACTION16chain 'B' and (resid 192 through 232 )
17X-RAY DIFFRACTION17chain 'B' and (resid 233 through 248 )

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