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- PDB-6atx: Crystal structure of Physcomitrella patens KAI2-like C -

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Basic information

Entry
Database: PDB / ID: 6atx
TitleCrystal structure of Physcomitrella patens KAI2-like C
ComponentsPpKAI2-like C
KeywordsHYDROLASE / alpha/beta hydrolase / strigolactone binding
Function / homologyAlpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Predicted protein
Function and homology information
Biological speciesPhyscomitrella patens subsp. patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74033790814 Å
AuthorsBurger, M. / Lee, H.J. / Chory, J.
CitationJournal: Cell Rep / Year: 2019
Title: Structural Basis of Karrikin and Non-natural Strigolactone Perception in Physcomitrella patens.
Authors: Burger, M. / Mashiguchi, K. / Lee, H.J. / Nakano, M. / Takemoto, K. / Seto, Y. / Yamaguchi, S. / Chory, J.
History
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PpKAI2-like C


Theoretical massNumber of molelcules
Total (without water)30,4041
Polymers30,4041
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.630, 46.630, 140.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein PpKAI2-like C


Mass: 30403.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrella patens subsp. patens (plant)
Gene: PHYPADRAFT_213263 / Plasmid: pGEX4T3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A9SKF7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.2 M ammonium sulfate, 0.2 M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2016 / Details: mirror
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: 2.74→46.63 Å / Num. obs: 7881 / % possible obs: 99.92 % / Redundancy: 13.7 % / Biso Wilson estimate: 37.0104001296 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.2201 / Rpim(I) all: 0.06161 / Net I/σ(I): 12.35
Reflection shellResolution: 2.74→2.84 Å / Rmerge(I) obs: 0.8344 / CC1/2: 0.504 / Rpim(I) all: 0.2964

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4IH1

4ih1


Resolution: 2.74033790814→46.63 Å / SU ML: 0.391600951074 / Cross valid method: FREE R-VALUE / σ(F): 1.35078110119 / Phase error: 22.6905586875
RfactorNum. reflection% reflection
Rfree0.219014953825 399 5.06280928816 %
Rwork0.177501886647 --
obs0.179600563238 7881 99.9365965001 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.3194246999 Å2
Refinement stepCycle: LAST / Resolution: 2.74033790814→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 0 42 2103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002860085055112111
X-RAY DIFFRACTIONf_angle_d0.5960300143512877
X-RAY DIFFRACTIONf_chiral_restr0.0440365621065334
X-RAY DIFFRACTIONf_plane_restr0.00358640620628369
X-RAY DIFFRACTIONf_dihedral_angle_d2.724639086741244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7403-3.13680.3142906916761360.2467411846022485X-RAY DIFFRACTION100
3.1368-3.95170.2156406996841270.1830745189982475X-RAY DIFFRACTION99.9615827891
3.9517-46.63670.1773657504091360.1441683703172522X-RAY DIFFRACTION99.8872604284

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