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- PDB-5dnu: Crystal structure of Striga KAI2-like protein in complex with karrikin -

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Basic information

Entry
Database: PDB / ID: 5dnu
TitleCrystal structure of Striga KAI2-like protein in complex with karrikin
ComponentsShKAI2iB
KeywordsHYDROLASE / KAI2 Karrikin Striga
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
BENZOIC ACID / FORMIC ACID / 3-methyl-2H-furo[2,3-c]pyran-2-one / Hyposensitive to light 3
Similarity search - Component
Biological speciesStriga hermonthica (purple witchweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsXu, Y. / Miyakawa, T. / Nakamura, A. / Tanokura, M.
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis of unique ligand specificity of KAI2-like protein from parasitic weed Striga hermonthica
Authors: Xu, Y. / Miyakawa, T. / Nakamura, H. / Nakamura, A. / Imamura, Y. / Asami, T. / Tanokura, M.
History
DepositionSep 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Aug 28, 2019Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / pdbx_struct_oper_list / pdbx_struct_special_symmetry
Item: _chem_comp.pdbx_synonyms / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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 / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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

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Assembly

Deposited unit
A: ShKAI2iB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,31020
Polymers30,2441
Non-polymers1,06619
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-20 kcal/mol
Surface area11440 Å2
Unit cell
Length a, b, c (Å)75.757, 75.757, 181.266
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-319-

BEZ

21A-319-

BEZ

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ShKAI2iB


Mass: 30244.414 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: A0A0M3PN85*PLUS

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Non-polymers , 6 types, 228 molecules

#2: Chemical ChemComp-KKN / 3-methyl-2H-furo[2,3-c]pyran-2-one / Karrikin KAR1


Mass: 150.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Sodium formate, Tris

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→19.7 Å / Num. obs: 96642 / % possible obs: 99.9 % / Redundancy: 20.6 % / Net I/σ(I): 97.8
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DNW

5dnw


Resolution: 1.2→19.7 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.862 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15539 4887 5.1 %RANDOM
Rwork0.14009 ---
obs0.14089 91454 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.067 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.2→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 70 209 2355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192210
X-RAY DIFFRACTIONr_bond_other_d0.0020.022089
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.962987
X-RAY DIFFRACTIONr_angle_other_deg1.0573.0014777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.70922.8100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69815341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4961518
X-RAY DIFFRACTIONr_chiral_restr0.1020.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212523
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02542
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_it2.2392.0171077
X-RAY DIFFRACTIONr_mcbond_other2.242.0181078
X-RAY DIFFRACTIONr_mcangle_it2.6663.0351347
X-RAY DIFFRACTIONr_mcangle_other2.6733.0391348
X-RAY DIFFRACTIONr_scbond_it2.2742.2811133
X-RAY DIFFRACTIONr_scbond_other2.2732.281134
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6653.311636
X-RAY DIFFRACTIONr_long_range_B_refined3.50117.8172712
X-RAY DIFFRACTIONr_long_range_B_other3.517.8152713
X-RAY DIFFRACTIONr_rigid_bond_restr2.14334298
X-RAY DIFFRACTIONr_sphericity_free30.658557
X-RAY DIFFRACTIONr_sphericity_bonded12.86354413
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 350 -
Rwork0.193 6607 -
obs--99.58 %

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