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- PDB-7f5w: Conserved and divergent strigolactone signaling in Saccharum spon... -

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Basic information

Entry
Database: PDB / ID: 7f5w
TitleConserved and divergent strigolactone signaling in Saccharum spontaneum
ComponentsHigh tillering and dwarf 2 protein
KeywordsPLANT PROTEIN / hydrolase protein DWARF 14 SL RECEPTOR
Function / homologyStrigolactone esterase D14 family / lysophospholipase / strigolactone biosynthetic process / secondary shoot formation / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / High tillering and dwarf 2 protein
Function and homology information
Biological speciesSaccharum hybrid cultivar ROC22 (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.654 Å
AuthorsZhao, Q.Q. / Ming, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31700052 China
CitationJournal: Front Plant Sci / Year: 2021
Title: Identification of Conserved and Divergent Strigolactone Receptors in Sugarcane Reveals a Key Residue Crucial for Plant Branching Control.
Authors: Hu, A. / Zhao, Q. / Chen, L. / Zhao, J. / Wang, Y. / Feng, K. / Wu, L. / Xie, M. / Zhou, X. / Xiao, L. / Ming, Z. / Zhang, M. / Yao, R.
History
DepositionJun 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 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: High tillering and dwarf 2 protein
B: High tillering and dwarf 2 protein


Theoretical massNumber of molelcules
Total (without water)65,6112
Polymers65,6112
Non-polymers00
Water6,431357
1
A: High tillering and dwarf 2 protein


Theoretical massNumber of molelcules
Total (without water)32,8051
Polymers32,8051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: High tillering and dwarf 2 protein


Theoretical massNumber of molelcules
Total (without water)32,8051
Polymers32,8051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.810, 88.295, 118.521
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 High tillering and dwarf 2 protein


Mass: 32805.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharum hybrid cultivar ROC22 (plant)
Gene: HTD2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0D5NT23
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 1.92 Å3/Da / Density % sol: 35.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.01 M Magnesium chloride hexahydrate, 0.05 M TRIS hydrochloride pH 7.5, 5% v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.65→70.81 Å / Num. obs: 110054 / % possible obs: 93.6 % / Redundancy: 6.144 % / Rrim(I) all: 0.115 / Net I/σ(I): 12.1
Reflection shellResolution: 1.65→1.74 Å / Rmerge(I) obs: 0.744 / Num. unique obs: 58049

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VXK

3vxk


Resolution: 1.654→70.806 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 3790 3.44 %
Rwork0.1914 106264 -
obs0.1927 110054 93.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.15 Å2 / Biso mean: 28.3539 Å2 / Biso min: 9.33 Å2
Refinement stepCycle: final / Resolution: 1.654→70.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4151 0 0 357 4508
Biso mean---36.89 -
Num. residues----537
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6544-1.67540.39821520.3477411698
1.6754-1.69740.41741400.3402415198
1.6974-1.72070.33151500.3167417399
1.7207-1.74520.35071530.3215424299
1.7452-1.77130.40011460.31344203100
1.7713-1.7990.31961510.29454203100
1.799-1.82850.35661530.28664223100
1.8285-1.860.35081530.2762418199
1.86-1.89380.27921480.25964173100
1.8938-1.93030.2965550.2523159938
1.9303-1.96970.25651500.23334263100
1.9697-2.01250.25431540.22924184100
2.0125-2.05930.25431280.2272360199
2.0593-2.11080.235310.201691891
2.1108-2.16790.19351500.19234183100
2.1679-2.23170.23931510.1954239100
2.2317-2.30370.25231510.19654197100
2.3037-2.38610.21441500.1794226100
2.3861-2.48160.25481430.19074195100
2.4816-2.59450.2021530.19034256100
2.5945-2.73130.22221520.1844240100
2.7313-2.90250.24791440.18644191100
2.9025-3.12660.20241520.17714220100
3.1266-3.44120.22791470.1717399699
3.4412-3.93910.21871320.1565366789
3.9391-4.96270.16131540.1414238100
4.9627-4.96650.17711470.168418699
Refinement TLS params.Method: refined / Origin x: 22.4898 Å / Origin y: 2.9856 Å / Origin z: -4.7336 Å
111213212223313233
T0.0834 Å20.0232 Å2-0.0113 Å2-0.1121 Å2-0.0221 Å2--0.1126 Å2
L0.1212 °20.135 °2-0.1864 °2-0.414 °2-0.1198 °2--0.472 °2
S-0.0489 Å °-0.0062 Å °-0.01 Å °-0.0506 Å °0.0513 Å °-0.0439 Å °0.1244 Å °0.0226 Å °0.0049 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 268
2X-RAY DIFFRACTION1allB1 - 268
3X-RAY DIFFRACTION1allS1 - 357

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