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- PDB-5cbk: Crystal structure of the strigolactone receptor ShHTL5 from Strig... -

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Basic information

Entry
Database: PDB / ID: 5cbk
TitleCrystal structure of the strigolactone receptor ShHTL5 from Striga hermonthica
ComponentsShHTL5
KeywordsSIGNALING PROTEIN / Striga hermonthica / strigolactone / signalling / receptor / ShHTL5 / alpha/beta hydrolase
Function / homology
Function and homology information


Alpha/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
Similarity search - Domain/homology
Chem-PE3 / Hyposensitive to light 5
Similarity search - Component
Biological speciesStriga hermonthica (purple witchweed)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.462 Å
AuthorsStogios, P.J. / Onopriyenko, O. / Yim, V. / Savchenko, A.
CitationJournal: Science / Year: 2015
Title: Structure-function analysis identifies highly sensitive strigolactone receptors in Striga.
Authors: Toh, S. / Holbrook-Smith, D. / Stogios, P.J. / Onopriyenko, O. / Lumba, S. / Tsuchiya, Y. / Savchenko, A. / McCourt, P.
History
DepositionJul 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ShHTL5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3205
Polymers29,9911
Non-polymers1,3294
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-26 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.282, 102.282, 101.734
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-662-

HOH

21A-663-

HOH

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Components

#1: Protein ShHTL5


Mass: 29991.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Striga hermonthica (purple witchweed) / Gene: ShHTL5 / Plasmid: p15Tv LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M5I297*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL / Polyethylene glycol


Mass: 634.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H58O15
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.7 M sodium citrate, 0.01 M magnesium chloride, 0.05 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→29.527 Å / Num. obs: 14453 / % possible obs: 100 % / Redundancy: 20.3 % / Rsym value: 0.099 / Net I/σ(I): 53.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 19.1 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W06

3w06


Resolution: 2.462→29.526 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 589 4.99 %Random selection
Rwork0.1684 ---
obs0.1712 11812 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.462→29.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 28 300 2433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032212
X-RAY DIFFRACTIONf_angle_d0.7542997
X-RAY DIFFRACTIONf_dihedral_angle_d14.069817
X-RAY DIFFRACTIONf_chiral_restr0.026336
X-RAY DIFFRACTIONf_plane_restr0.003390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4625-2.71010.25481440.20682724X-RAY DIFFRACTION99
2.7101-3.10190.26871440.19652763X-RAY DIFFRACTION100
3.1019-3.90660.24531460.16882776X-RAY DIFFRACTION99
3.9066-29.52840.18461550.1472960X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3292-0.5897-0.20851.90840.1333.5369-0.0880.12380.2523-0.1021-0.0897-0.2203-0.28210.42270.11670.2533-0.0851-0.04850.28040.06550.342-6.955443.5273-3.5019
24.10432.37872.73816.43784.1294.56380.12240.3284-0.40810.3588-0.0137-0.08780.45990.2723-0.10240.2225-0.01230.02310.29840.04620.2844-7.103825.4633-1.1774
37.5304-0.23081.17996.23620.06296.5989-0.07440.4688-0.1394-0.3088-0.05460.2990.0365-0.26390.15220.3205-0.0824-0.07230.2308-0.02210.2134-18.443930.6612-14.2914
44.3941-0.3799-0.31983.10870.492.1519-0.02950.0272-0.00290.1212-0.11380.05780.00750.01240.11960.2403-0.0417-0.0010.25410.05680.2268-13.152830.71567.9743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 1:103
2X-RAY DIFFRACTION2chain A and resi 104:146
3X-RAY DIFFRACTION3chain A and resi 147:193
4X-RAY DIFFRACTION4chain A and resi 194:271

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