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- PDB-5z8p: Structural basis for specific inhibition of highly sensitive ShHT... -

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Basic information

Entry
Database: PDB / ID: 5z8p
TitleStructural basis for specific inhibition of highly sensitive ShHTL7 receptor
ComponentsHyposensitive to light 7
KeywordsHYDROLASE / Strigolactone receptor / Striga germination signaling
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 / metal ion binding / Alpha Beta / Hyposensitive to light 7
Function and homology information
Biological speciesStriga hermonthica (purple witchweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHameed, U.S. / Arold, S.T.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
King Abdullah University of Science and Technology Saudi Arabia
CitationJournal: EMBO Rep. / Year: 2018
Title: Structural basis for specific inhibition of the highly sensitive ShHTL7 receptor.
Authors: Shahul Hameed, U. / Haider, I. / Jamil, M. / Kountche, B.A. / Guo, X. / Zarban, R.A. / Kim, D. / Al-Babili, S. / Arold, S.T.
History
DepositionFeb 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _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_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hyposensitive to light 7


Theoretical massNumber of molelcules
Total (without water)30,6101
Polymers30,6101
Non-polymers00
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11610 Å2
Unit cell
Length a, b, c (Å)92.590, 92.590, 80.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Hyposensitive to light 7 / ShHTL7


Mass: 30610.168 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: A0A0M3PNA2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 3.19 Å3/Da / Density % sol: 61.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES monohydrate pH 6.5, 1.6 M Magnesium sulfate heptahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.35→40.09 Å / Num. obs: 85478 / % possible obs: 99.61 % / Redundancy: 9.1 % / CC1/2: 0.999 / Net I/σ(I): 23.12
Reflection shellResolution: 1.35→1.398 Å / CC1/2: 0.575

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Processing

Software
NameVersionClassification
REFMAC5.8.0210refinement
PROTEUM PLUSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CBK

5cbk


Resolution: 1.35→40.09 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.415 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14379 4274 5 %RANDOM
Rwork0.12835 ---
obs0.12913 81206 99.7 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.335 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.13 Å2-0 Å2
2---0.25 Å20 Å2
3---0.82 Å2
Refinement stepCycle: 1 / Resolution: 1.35→40.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 0 269 2357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192254
X-RAY DIFFRACTIONr_bond_other_d0.0010.022081
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9773085
X-RAY DIFFRACTIONr_angle_other_deg0.84734843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7795293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77723.84691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1615380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0651511
X-RAY DIFFRACTIONr_chiral_restr0.0880.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212550
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02445
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0851.721139
X-RAY DIFFRACTIONr_mcbond_other1.0611.7171138
X-RAY DIFFRACTIONr_mcangle_it1.4752.5911443
X-RAY DIFFRACTIONr_mcangle_other1.4842.5941444
X-RAY DIFFRACTIONr_scbond_it1.7352.0881115
X-RAY DIFFRACTIONr_scbond_other1.7222.0791113
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3013.0031642
X-RAY DIFFRACTIONr_long_range_B_refined3.96523.0672629
X-RAY DIFFRACTIONr_long_range_B_other2.76321.9112549
X-RAY DIFFRACTIONr_rigid_bond_restr1.7734335
X-RAY DIFFRACTIONr_sphericity_free31.6125192
X-RAY DIFFRACTIONr_sphericity_bonded9.94854370
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 304 -
Rwork0.438 5759 -
obs--96.09 %

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