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- PDB-6azc: Crystal structure of Physcomitrella patens KAI2-like E S166A -

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Basic information

Entry
Database: PDB / ID: 6azc
TitleCrystal structure of Physcomitrella patens KAI2-like E S166A
ComponentsPp-KAI2-like E
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 / hydrolase activity / 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: 2.00001213332 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pp-KAI2-like E
B: Pp-KAI2-like E


Theoretical massNumber of molelcules
Total (without water)59,7582
Polymers59,7582
Non-polymers00
Water2,882160
1
A: Pp-KAI2-like E


Theoretical massNumber of molelcules
Total (without water)29,8791
Polymers29,8791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pp-KAI2-like E


Theoretical massNumber of molelcules
Total (without water)29,8791
Polymers29,8791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.932, 121.821, 46.909
Angle α, β, γ (deg.)90.000, 91.539, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEU(chain 'A' and (resid 6 through 100 or resid 102 through 268))AA6 - 998 - 101
12VALVAL(chain 'A' and (resid 6 through 100 or resid 102 through 268))AA102 - 267104 - 269
21LEULEU(chain 'B' and (resid 6 through 100 or resid 102 through 268))BB6 - 998 - 101
22VALVAL(chain 'B' and (resid 6 through 100 or resid 102 through 268))BB102 - 267104 - 269

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Components

#1: Protein Pp-KAI2-like E


Mass: 29879.115 Da / Num. of mol.: 2 / Mutation: S166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrella patens subsp. patens (plant)
Gene: PHYPADRAFT_215526 / Plasmid: pGEX4T3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A9ST85, Hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 30% PEG8000

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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 17, 2017 / 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: 2→46.9 Å / Num. obs: 35204 / % possible obs: 98.73 % / Redundancy: 3.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.07743 / Rpim(I) all: 0.04693 / Net I/σ(I): 11.52
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.132 / Mean I/σ(I) obs: 8.12 / Num. unique obs: 3382 / CC1/2: 0.966 / Rpim(I) all: 0.07907 / % 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 6AZB

6azb


Resolution: 2.00001213332→46.8922764945 Å / Cross valid method: FREE R-VALUE / σ(F): 5.13869702 / Phase error: 36.7910091517
RfactorNum. reflection% reflection
Rfree0.253384709586 1767 5.14950166113 %
Rwork0.219885252492 --
obs0.262794476922 34314 98.733958681 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.358351877 Å2
Refinement stepCycle: LAST / Resolution: 2.00001213332→46.8922764945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 0 160 4238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002974192272984184
X-RAY DIFFRACTIONf_angle_d0.5913956583785697
X-RAY DIFFRACTIONf_chiral_restr0.0472862199619655
X-RAY DIFFRACTIONf_plane_restr0.00414553025847735
X-RAY DIFFRACTIONf_dihedral_angle_d2.201173915842932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05890.3800388129691380.3522098546122639X-RAY DIFFRACTION92.5640126271
2.0589-2.12530.359914647511410.3334245780442697X-RAY DIFFRACTION93.2250259246
2.1253-2.20120.3616876051281450.3122735454392706X-RAY DIFFRACTION93.536121673
2.2012-2.28920.3531808564681330.3146699978142715X-RAY DIFFRACTION93.7176389368
2.2892-2.39330.3591618373971400.3043374333912682X-RAY DIFFRACTION93.5799023029
2.3933-2.51920.3399539539851380.2958501283622714X-RAY DIFFRACTION93.9425406715
2.5192-2.67680.3278296206681500.2867430941892715X-RAY DIFFRACTION93.75
2.6768-2.8830.262214303721400.2810969396162728X-RAY DIFFRACTION94.2965779468
2.883-3.17230.3091390983541500.2445126010272715X-RAY DIFFRACTION93.75
3.1723-3.62930.2482752116741510.2250908565792736X-RAY DIFFRACTION94.2798070296
3.6293-4.56490.2449792716861450.1888937366142751X-RAY DIFFRACTION94.7314049587
4.5649-21.11340.2461856384791490.2077662545522768X-RAY DIFFRACTION94.1176470588

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