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- PDB-6j2r: Crystal structure of Striga hermonthica HTL8 (ShHTL8) -

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Basic information

Entry
Database: PDB / ID: 6j2r
TitleCrystal structure of Striga hermonthica HTL8 (ShHTL8)
ComponentsHyposensitive to light 8
KeywordsPLANT PROTEIN / Striga hermonthica / HTL8
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 / Hyposensitive to light 8
Function and homology information
Biological speciesStriga hermonthica (purple witchweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsZhang, Y.Y. / Xi, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21332004 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure and biochemical characterization of Striga hermonthica HYPO-SENSITIVE TO LIGHT 8 (ShHTL8) in strigolactone signaling pathway.
Authors: Zhang, Y. / Wang, D. / Shen, Y. / Xi, Z.
History
DepositionJan 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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: Hyposensitive to light 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2122
Polymers30,1201
Non-polymers921
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.628, 83.483, 84.077
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 8


Mass: 30120.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Striga hermonthica (purple witchweed) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4APJ4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M ammonium formate, 20% (w/v) PEG 3500 and 0.1 M ADA pH 6.6
PH range: 5.5-7.5 / Temp details: 303

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.399→50 Å / Num. obs: 58744 / % possible obs: 95.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.038 / Rrim(I) all: 0.088 / Χ2: 0.98 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.4220.30820390.8260.2560.4041.01167.3
1.42-1.452.30.30923150.8670.2350.3911.05676
1.45-1.482.60.28125520.8850.2040.351.03784.2
1.48-1.5130.2527720.9150.1670.3031.12190.9
1.51-1.543.40.21828770.950.1320.2571.02194.9
1.54-1.584.10.21329740.9540.1150.2431.05998
1.58-1.625.40.19530510.9690.0910.2151.10799.9
1.62-1.665.60.17730300.9750.0810.1951.127100
1.66-1.715.60.15830510.9790.0720.1741.08199.8
1.71-1.765.50.14130280.9810.0650.1551.07799.9
1.76-1.8350.12930700.980.0620.1431.09799.7
1.83-1.95.60.11930650.9830.0540.1311.11699.9
1.9-1.995.60.10630630.9810.0490.1170.997100
1.99-2.095.40.09930520.9870.0460.1090.94399.9
2.09-2.225.10.09230690.9870.0450.1030.99699.9
2.22-2.395.70.08630890.9890.0390.0940.87499.9
2.39-2.635.50.07931240.990.0360.0870.82199.9
2.63-3.025.30.07630980.9910.0350.0840.79899.8
3.02-3.85.50.07131560.990.0330.0780.84199.7
3.8-105.10.06132690.9930.0290.0680.69697.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A9D

6a9d


Resolution: 1.4→30.161 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.79
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.1862 2963 5.21 %
Rwork0.1711 --
obs0.1719 56868 92.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.68 Å2 / Biso mean: 19.2301 Å2 / Biso min: 8.12 Å2
Refinement stepCycle: final / Resolution: 1.4→30.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 6 267 2342
Biso mean--23.59 32.14 -
Num. residues----267
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.42150.3511560.2473115742
1.4215-1.4460.2672770.2389158457
1.446-1.47230.22591120.2234198273
1.4723-1.50060.22151290.2157234585
1.5006-1.53120.21521300.1986251793
1.5312-1.56450.20741530.1922266897
1.5645-1.60090.19381570.1811273199
1.6009-1.6410.17831550.17442721100
1.641-1.68530.19391350.17112781100
1.6853-1.73490.19881690.17142695100
1.7349-1.79090.16871510.16872749100
1.7909-1.85490.18951600.17062766100
1.8549-1.92920.16441650.16232721100
1.9292-2.01690.16791620.15872764100
2.0169-2.12320.19071590.16052749100
2.1232-2.25620.16791510.16112789100
2.2562-2.43040.18841510.1612798100
2.4304-2.67480.18781550.1682782100
2.6748-3.06150.21041640.17632806100
3.0615-3.8560.16771290.15942862100
3.856-100.18011430.1765293897
Refinement TLS params.Method: refined / Origin x: 13.2178 Å / Origin y: -3.4967 Å / Origin z: -0.8207 Å
111213212223313233
T0.1047 Å20.002 Å2-0.0018 Å2-0.1305 Å20.0042 Å2--0.0662 Å2
L0.6702 °2-0.0507 °2-0.0856 °2-0.4457 °2-0.0527 °2--1.9543 °2
S-0.0111 Å °-0.0315 Å °-0.0059 Å °0.0341 Å °0.031 Å °-0.0177 Å °0.0108 Å °0.0145 Å °-0.0245 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 269
2X-RAY DIFFRACTION1allA401
3X-RAY DIFFRACTION1allS1 - 267

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