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- PDB-7k2z: Crystal structure of Pisum sativum KAI2 Apo form -

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Basic information

Entry
Database: PDB / ID: 7k2z
TitleCrystal structure of Pisum sativum KAI2 Apo form
ComponentsPsKAI2B protein
KeywordsHYDROLASE / enzyme / karrikin / receptor / a/b hydrolase
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 9, 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)30,1452
Polymers30,0521
Non-polymers921
Water5,026279
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)87.595, 71.146, 49.065
Angle α, β, γ (deg.)90.000, 117.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

21A-743-

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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.43 %
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: 1.61→43.47 Å / Num. obs: 34306 / % possible obs: 99.2 % / Redundancy: 6.4 % / CC1/2: 1 / Net I/σ(I): 31.01
Reflection shellResolution: 1.61→1.668 Å / Num. unique obs: 3156 / CC1/2: 0.746

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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: 1.61→43.47 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1796 2000 5.83 %
Rwork0.156 32306 -
obs0.1574 34306 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.71 Å2 / Biso mean: 21.3714 Å2 / Biso min: 10.72 Å2
Refinement stepCycle: final / Resolution: 1.61→43.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 6 279 2395
Biso mean--33.73 32.07 -
Num. residues----270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.61-1.650.27451180.2366191683
1.65-1.690.22321440.20162314100
1.69-1.740.21661440.18222329100
1.74-1.80.21311430.17432318100
1.8-1.860.22781440.17562327100
1.86-1.940.20761460.16442339100
1.94-2.030.19851440.15792336100
2.03-2.130.19711450.15152328100
2.13-2.270.18031430.14872324100
2.27-2.440.17311450.1522348100
2.44-2.690.17191450.15492334100
2.69-3.070.19261440.15612342100
3.07-3.870.15131460.14312347100
3.87-4.3470.15691490.14842404100

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