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- PDB-5gyy: Plant receptor complex -

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Basic information

Entry
Database: PDB / ID: 5gyy
TitlePlant receptor complex
Components
  • S-locus protein 11
  • S-receptor kinase SRK9
KeywordsPLANT PROTEIN / plant receptor / ligand
Function / homology
Function and homology information


rejection of self pollen / defense response to fungus / killing of cells of another organism / protein serine/threonine kinase activity / signal transduction / extracellular region / ATP binding / membrane
Similarity search - Function
S-locus glycoprotein domain / S-locus receptor kinase, C-terminal / S-locus, receptor kinase / S-receptor-like serine/threonine-protein kinase / S-locus glycoprotein domain / D-mannose binding lectin / PAN-like domain / Domain of unknown function (DUF3403) / Receptor serine/threonine kinase / Plant self-incompatibility response ...S-locus glycoprotein domain / S-locus receptor kinase, C-terminal / S-locus, receptor kinase / S-receptor-like serine/threonine-protein kinase / S-locus glycoprotein domain / D-mannose binding lectin / PAN-like domain / Domain of unknown function (DUF3403) / Receptor serine/threonine kinase / Plant self-incompatibility response / Plant self-incompatibility response (SCRL) protein / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / divergent subfamily of APPLE domains / Knottins / Knottin, scorpion toxin-like / PAN/Apple domain profile. / PAN/Apple domain / Knottin, scorpion toxin-like 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
Similarity search - Domain/homology
S-receptor kinase SRK9 / S-locus protein 11
Similarity search - Component
Biological speciesBrassica rapa subsp. oleifera (biennial turnip rape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.351 Å
AuthorsMa, R. / Han, Z. / Hu, Z. / Lin, G. / Gong, X. / Zhang, H. / June, N. / Chai, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation of China31130063 China
Chinese Ministry of Science and Technology2015CB910200 China
CitationJournal: To Be Published
Title: Plant receptor complex at 2.35 Angstroms resolution
Authors: Ma, R. / Han, Z. / Hu, Z. / Lin, G. / Gong, X. / Zhang, H. / June, N. / Chai, J.
History
DepositionSep 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 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

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Assembly

Deposited unit
A: S-receptor kinase SRK9
B: S-receptor kinase SRK9
G: S-locus protein 11
H: S-locus protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1026
Polymers104,6604
Non-polymers4422
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-18 kcal/mol
Surface area40290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.249, 135.121, 153.907
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 S-receptor kinase SRK9


Mass: 45864.707 Da / Num. of mol.: 2 / Fragment: UNP residues 28-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica rapa subsp. oleifera (biennial turnip rape)
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7DN95
#2: Protein S-locus protein 11


Mass: 6465.285 Da / Num. of mol.: 2 / Fragment: UNP residues 24-78
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica rapa subsp. oleifera (biennial turnip rape)
Gene: SP11 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9ST12
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 3.12 Å3/Da / Density % sol: 60.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: sodium malonate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→39.59 Å / Num. obs: 52223 / % possible obs: 95.1 % / Redundancy: 6.9 % / Net I/σ(I): 30

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.351→39.59 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.37
RfactorNum. reflection% reflection
Rfree0.2536 2594 5.04 %
Rwork0.1957 --
obs0.1987 51509 93.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.351→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7267 0 28 406 7701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087489
X-RAY DIFFRACTIONf_angle_d1.27810139
X-RAY DIFFRACTIONf_dihedral_angle_d13.4572709
X-RAY DIFFRACTIONf_chiral_restr0.0871103
X-RAY DIFFRACTIONf_plane_restr0.0061305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3515-2.39420.35841460.25382600X-RAY DIFFRACTION96
2.3942-2.44030.31551140.24792630X-RAY DIFFRACTION97
2.4403-2.49010.35891380.22862638X-RAY DIFFRACTION97
2.4901-2.54420.34421560.22462571X-RAY DIFFRACTION97
2.5442-2.60340.33771130.22712649X-RAY DIFFRACTION96
2.6034-2.66850.29631250.22782619X-RAY DIFFRACTION97
2.6685-2.74060.34641420.23682577X-RAY DIFFRACTION96
2.7406-2.82120.32751270.22142659X-RAY DIFFRACTION97
2.8212-2.91230.29241570.21422581X-RAY DIFFRACTION96
2.9123-3.01630.25961490.20952590X-RAY DIFFRACTION96
3.0163-3.13710.27431340.2092618X-RAY DIFFRACTION96
3.1371-3.27980.27041530.20262596X-RAY DIFFRACTION96
3.2798-3.45260.24861550.19732593X-RAY DIFFRACTION95
3.4526-3.66880.23921320.18292564X-RAY DIFFRACTION94
3.6688-3.95180.21831510.16922518X-RAY DIFFRACTION93
3.9518-4.3490.19481350.16162505X-RAY DIFFRACTION91
4.349-4.97730.20441190.14952467X-RAY DIFFRACTION88
4.9773-6.26680.17881180.17172451X-RAY DIFFRACTION87
6.2668-39.59540.23461300.2092489X-RAY DIFFRACTION84
Refinement TLS params.Method: refined / Origin x: 26.0585 Å / Origin y: 2.6464 Å / Origin z: 25.5532 Å
111213212223313233
T-0.0315 Å20.0187 Å2-0.0356 Å2-0.0055 Å20.0166 Å2--0.0495 Å2
L0.0954 °20.0163 °20.0174 °2-0.0412 °20.0499 °2--0.1151 °2
S-0.0208 Å °0.0202 Å °0.0341 Å °-0.0151 Å °0.0265 Å °0.0509 Å °-0.1181 Å °0.0205 Å °0.0403 Å °
Refinement TLS groupSelection details: all

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