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- PDB-7wa8: Strigolactone receptors in Striga ShHTL7 -

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Basic information

Entry
Database: PDB / ID: 7wa8
TitleStrigolactone receptors in Striga ShHTL7
ComponentsHyposensitive to light 7
KeywordsHYDROLASE / Receptor
Function / homologyAlpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Hyposensitive to light 7
Function and homology information
Biological speciesStriga hermonthica (purple witchweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsWang, Y. / Yao, R.
Funding support Australia, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070321 Australia
Other government2016YFA0500501 Australia
Other government2019RS2019 Australia
Other government2020JJ3007 Australia
Other government2018VBA0025 Australia
Australian Research Council (ARC)CE200100015 Australia
CitationJournal: Plant Physiology / Year: 2021
Title: Molecular basis for high ligand sensitivity and selectivity of strigolactone receptors in Striga.
Authors: Xie, D. / Smith, M.S. / Yao, R. / Wang, Y.
History
DepositionDec 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Hyposensitive to light 7
B: Hyposensitive to light 7


Theoretical massNumber of molelcules
Total (without water)60,3972
Polymers60,3972
Non-polymers00
Water1,42379
1
A: Hyposensitive to light 7


Theoretical massNumber of molelcules
Total (without water)30,1991
Polymers30,1991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hyposensitive to light 7


Theoretical massNumber of molelcules
Total (without water)30,1991
Polymers30,1991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.573, 78.338, 90.923
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hyposensitive to light 7 / HTL7 protein


Mass: 30198.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Striga hermonthica (purple witchweed) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3PNA2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 44.06 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 4mM calcium chloride, 20mM sodium acetate pH 4.6, 6% (v/v) (+/-)-2-Methyl-2,4-pentanediol, 160mM magnesium chloride, 80mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 23355 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.045 / Rrim(I) all: 0.119 / Χ2: 1.925 / Net I/σ(I): 10.6 / Num. measured all: 164850
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.33-2.376.80.61111430.8640.2510.6611.28699.9
2.37-2.417.10.53811450.9150.2160.5811.371100
2.41-2.467.20.49311530.9290.1970.5311.351100
2.46-2.517.20.44811490.9420.1780.4831.443100
2.51-2.567.30.39711380.950.1570.4271.427100
2.56-2.627.30.38311480.9490.1520.4121.389100
2.62-2.697.30.31111550.9730.1230.3351.545100
2.69-2.767.30.28311630.9690.1120.3051.551100
2.76-2.847.20.24111360.9810.0960.261.651100
2.84-2.947.20.211650.9870.080.2151.714100
2.94-3.047.30.16911380.9890.0670.1821.694100
3.04-3.167.30.13111750.9960.0520.1411.69100
3.16-3.317.20.1111550.9940.0440.1191.869100
3.31-3.487.20.09111700.9950.0360.0981.968100
3.48-3.77.20.07411710.9970.030.082.122100
3.7-3.987.10.06811740.9970.0270.0732.36499.9
3.98-4.386.90.06711810.9950.0270.0723.051100
4.38-5.026.50.06211980.9960.0260.0673.332100
5.02-6.326.60.06412060.9960.0270.072.968100
6.32-506.20.05312920.9980.0230.0582.92899.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z8P

5z8p


Resolution: 2.33→46.437 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2677 1188 5.1 %
Rwork0.1976 22112 -
obs0.2012 23300 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.11 Å2 / Biso mean: 36.7368 Å2 / Biso min: 16.74 Å2
Refinement stepCycle: final / Resolution: 2.33→46.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4153 0 1025 79 5257
Biso mean--37.84 36.51 -
Num. residues----401
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3304-2.43650.33591680.2099262998
2.4365-2.56490.31851370.21652739100
2.5649-2.72560.2781590.21812717100
2.7256-2.9360.30291410.21572760100
2.936-3.23140.26591420.19212744100
3.2314-3.69880.27271360.1822785100
3.6988-4.65940.22611390.17782824100
4.6594-46.40.25291660.20872914100

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