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- PDB-8hod: ScRIPK MUTANT-S253A, T254A -

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Basic information

Entry
Database: PDB / ID: 8hod
TitleScRIPK MUTANT-S253A, T254A
ComponentsHypothetical protein
KeywordsPLANT PROTEIN / Kinase / RLCK VII
Function / homology
Function and homology information


protein kinase activity / ATP binding
Similarity search - Function
: / 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. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Protein kinase domain-containing protein
Similarity search - Component
Biological speciesSaccharum hybrid cultivar (sugarcane)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFang, J.L. / Zhang, M.Q.
Funding support2items
OrganizationGrant numberCountry
Other governmentGuikeAA22117007
Other governmentCARS-170109
CitationJournal: Front Plant Sci / Year: 2023
Title: Receptor-like cytoplasmic kinase ScRIPK in sugarcane regulates disease resistance and drought tolerance in Arabidopsis.
Authors: Fang, J. / Chai, Z. / Huang, R. / Huang, C. / Ming, Z. / Chen, B. / Yao, W. / Zhang, M.
History
DepositionDec 9, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8345
Polymers36,1301
Non-polymers7034
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.820, 84.010, 98.810
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 Hypothetical protein


Mass: 36130.266 Da / Num. of mol.: 1 / Mutation: S252A, T253A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharum hybrid cultivar (sugarcane) / Gene: NCGR_LOCUS5996
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A811MS43
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 4.3 M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→84.01 Å / Num. obs: 27393 / % possible obs: 99.9 % / Redundancy: 12.478 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.031 / Rrim(I) all: 0.109 / Χ2: 0.98 / Net I/σ(I): 15.2
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.97 / Num. unique obs: 2012 / CC1/2: 0.835

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
PDB_EXTRACT4data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TOS

5tos


Resolution: 1.95→64.004 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 1959 7.28 %
Rwork0.1982 --
obs0.2005 26901 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→64.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 45 155 2392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072304
X-RAY DIFFRACTIONf_angle_d0.9673115
X-RAY DIFFRACTIONf_dihedral_angle_d10.7961366
X-RAY DIFFRACTIONf_chiral_restr0.055347
X-RAY DIFFRACTIONf_plane_restr0.005385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99880.3231310.27351694X-RAY DIFFRACTION94
1.9988-2.05280.30861290.25151688X-RAY DIFFRACTION95
2.0528-2.11320.331360.22831722X-RAY DIFFRACTION97
2.1132-2.18140.25681370.20781734X-RAY DIFFRACTION98
2.1814-2.25940.2411370.20021773X-RAY DIFFRACTION99
2.2594-2.34990.21371410.1921771X-RAY DIFFRACTION99
2.3499-2.45680.25131370.19081764X-RAY DIFFRACTION99
2.4568-2.58640.22041410.20541778X-RAY DIFFRACTION99
2.5864-2.74840.22581420.22031796X-RAY DIFFRACTION100
2.7484-2.96060.29381410.22731797X-RAY DIFFRACTION100
2.9606-3.25850.25111440.2161816X-RAY DIFFRACTION100
3.2585-3.730.21431430.1781819X-RAY DIFFRACTION100
3.73-4.69920.16271460.16351861X-RAY DIFFRACTION100
4.6992-640.22051540.19751929X-RAY DIFFRACTION99

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