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- PDB-6azd: Crystal structure of Physcomitrella patens KAI2-like H -

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Basic information

Entry
Database: PDB / ID: 6azd
TitleCrystal structure of Physcomitrella patens KAI2-like H
ComponentsPpKAI2-like H
KeywordsHYDROLASE / alpha/beta hydrolase / strigolactone binding
Function / homologyalpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / AB hydrolase-1 domain-containing protein
Function and homology information
Biological speciesPhyscomitrella patens subsp. patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97010740396 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
DepositionSep 11, 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

Downloads & links

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Assembly

Deposited unit
A: PpKAI2-like H


Theoretical massNumber of molelcules
Total (without water)29,8651
Polymers29,8651
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.410, 52.650, 52.300
Angle α, β, γ (deg.)90.000, 95.510, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein PpKAI2-like H


Mass: 29864.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrella patens subsp. patens (plant)
Gene: PHYPADRAFT_184560 / Plasmid: pGEX4T3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A9SG07, Hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.8 M ammonium sulfate, 0.1 M MES 6.5, 5% PEG400

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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: mirrors
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: 1.97→37.1 Å / Num. obs: 18745 / % possible obs: 98.31 % / Redundancy: 3.5 % / CC1/2: 0.982 / Rmerge(I) obs: 0.1674 / Rpim(I) all: 0.1065 / Net I/σ(I): 8.17
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4449 / Mean I/σ(I) obs: 3.85 / Num. unique obs: 1833 / CC1/2: 0.549 / Rpim(I) all: 0.285 / % possible all: 97.66

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4jyp


Resolution: 1.97010740396→37.0182176364 Å / SU ML: 0.277465883878 / Cross valid method: FREE R-VALUE / σ(F): 1.3487061327 / Phase error: 24.1330848868
RfactorNum. reflection% reflection
Rfree0.24287786124 930 4.96238194333 %
Rwork0.208001052653 --
obs0.209706317639 18741 98.3108639773 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.9028463926 Å2
Refinement stepCycle: LAST / Resolution: 1.97010740396→37.0182176364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 0 155 2218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003427302710522108
X-RAY DIFFRACTIONf_angle_d0.6048368063022872
X-RAY DIFFRACTIONf_chiral_restr0.0437368096835334
X-RAY DIFFRACTIONf_plane_restr0.00306973783748371
X-RAY DIFFRACTIONf_dihedral_angle_d2.660859468811247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9701-2.0740.3336100843691560.280668197122487X-RAY DIFFRACTION97.9977753059
2.074-2.20390.2748097083841300.2429091346482538X-RAY DIFFRACTION98.5228951256
2.2039-2.3740.3240741007661080.2305949199152552X-RAY DIFFRACTION98.4820436875
2.374-2.61290.264544976261260.2227036988472581X-RAY DIFFRACTION99.1212010253
2.6129-2.99080.2279934942541280.2115619954542543X-RAY DIFFRACTION98.9625787329
2.9908-3.76750.2260250466111610.1806869397712534X-RAY DIFFRACTION98.2859226842
3.7675-37.02470.1662155261151210.1696544989482576X-RAY DIFFRACTION96.909809558

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