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- PDB-7k38: Crystal structure of Pisum sativum KAI2 in complex with GR24-ent5... -

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Basic information

Entry
Database: PDB / ID: 7k38
TitleCrystal structure of Pisum sativum KAI2 in complex with GR24-ent5DS product
ComponentsPsKAI2B protein
KeywordsHYDROLASE / enzyme / karrikin / receptor / a/b hydrolase
Function / homology(5S)-5-hydroxy-3-methylfuran-2(5H)-one
Function and homology information
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGuercio, A.M. / Shabek, N.
CitationJournal: Commun Biol / Year: 2022
Title: Structural and functional analyses explain Pea KAI2 receptor diversity and reveal stereoselective catalysis during signal perception.
Authors: Guercio, A.M. / Torabi, S. / Cornu, D. / Dalmais, M. / Bendahmane, A. / Le Signor, C. / Pillot, J.P. / Le Bris, P. / Boyer, F.D. / Rameau, C. / Gutjahr, C. / de Saint Germain, A. / Shabek, N.
History
DepositionSep 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 2, 2022Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PsKAI2B protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1672
Polymers30,0521
Non-polymers1141
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.089, 71.820, 48.794
Angle α, β, γ (deg.)90.000, 117.300, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

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Components

#1: Protein PsKAI2B protein


Mass: 30052.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-VTY / (5S)-5-hydroxy-3-methylfuran-2(5H)-one


Mass: 114.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.5, 2.75% PEG 2000, 2.75% PEG 3350, 2.75% PEG 4000, 2.75% PEG-ME 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 17837 / % possible obs: 99 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.036 / Rrim(I) all: 0.089 / Χ2: 2.662 / Net I/σ(I): 13.7 / Num. measured all: 108361
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.034.50.3167200.9380.1580.3550.8381.3
2.03-2.075.20.2748960.950.1290.3041.1298.8
2.07-2.115.80.2378990.9660.1060.261.06499.9
2.11-2.156.20.2218770.9730.0960.2411.174100
2.15-2.26.20.1938890.9750.0830.2111.297100
2.2-2.256.20.1828970.980.0790.1981.292100
2.25-2.316.20.179120.9810.0740.1861.638100
2.31-2.376.30.1618750.9780.070.1761.715100
2.37-2.446.20.149140.9890.0620.1531.801100
2.44-2.526.30.1328950.9880.0580.1442.16100
2.52-2.616.30.129070.990.0520.1312.21100
2.61-2.716.30.1139080.990.0490.1232.564100
2.71-2.846.30.1028840.9920.0440.1123100
2.84-2.996.20.0949050.9930.0410.1023.343100
2.99-3.176.30.0868920.9940.0370.0933.992100
3.17-3.426.30.0778990.9940.0340.0844.508100
3.42-3.766.20.0729300.9940.0320.0795.092100
3.76-4.316.20.0668950.9940.0290.0725.655100
4.31-5.4360.0519140.9980.0230.0563.733100
5.43-506.10.0459290.9970.020.0493.617100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z9H

5z9h


Resolution: 2→43.36 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2141 1784 10.01 %
Rwork0.1681 16046 -
obs0.1727 17830 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.03 Å2 / Biso mean: 26.961 Å2 / Biso min: 11.82 Å2
Refinement stepCycle: final / Resolution: 2→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 14 180 2304
Biso mean--29.12 32.22 -
Num. residues----270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.060.23861150.20131031114684
2.06-2.120.27221400.192712601400100
2.12-2.190.25241360.18312291365100
2.19-2.260.25731380.176912391377100
2.26-2.350.22031400.180612621402100
2.35-2.460.24931380.177112381376100
2.46-2.590.26921370.181312331370100
2.59-2.750.24891390.189412461385100
2.75-2.970.26821390.193212511390100
2.97-3.260.22611390.181112521391100
3.26-3.740.18881400.158312701410100
3.74-4.710.17841400.132612441384100
4.71-43.360.15871430.154812911434100

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