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- PDB-5dnw: Crystal structure of KAI2-like protein from Striga (apo state 1) -

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Basic information

Entry
Database: PDB / ID: 5dnw
TitleCrystal structure of KAI2-like protein from Striga (apo state 1)
ComponentsShKAI2iB
KeywordsHYDROLASE / KAI2 Karrikin Striga
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 / FORMIC ACID / Hyposensitive to light 3
Function and homology information
Biological speciesStriga hermonthica (purple witchweed)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 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 1.2Nov 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 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_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)30,76013
Polymers30,2441
Non-polymers51512
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-22 kcal/mol
Surface area11820 Å2
Unit cell
Length a, b, c (Å)75.940, 75.940, 181.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#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) / Plasmid: pGEX6P-3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A0A0M3PN85*PLUS
#2: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.02→19.74 Å / Num. obs: 21039 / % possible obs: 99.6 % / Redundancy: 18.7 % / Net I/σ(I): 36.2
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 6.1 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VXK

3vxk


Resolution: 2.02→19.74 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.888 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22462 1080 5.1 %RANDOM
Rwork0.17743 ---
obs0.1798 19959 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.84 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.02→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2121 0 32 235 2388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192214
X-RAY DIFFRACTIONr_bond_other_d0.0020.022084
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9482999
X-RAY DIFFRACTIONr_angle_other_deg0.9534771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.945279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65322.92999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67615343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4671517
X-RAY DIFFRACTIONr_chiral_restr0.0770.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212549
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02538
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_it1.8332.8421110
X-RAY DIFFRACTIONr_mcbond_other1.8322.8441111
X-RAY DIFFRACTIONr_mcangle_it3.0864.2491391
X-RAY DIFFRACTIONr_mcangle_other3.0854.2521392
X-RAY DIFFRACTIONr_scbond_it1.9143.0871104
X-RAY DIFFRACTIONr_scbond_other1.9133.0871104
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1794.5141609
X-RAY DIFFRACTIONr_long_range_B_refined5.87723.9842677
X-RAY DIFFRACTIONr_long_range_B_other5.88623.9862678
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 67 -
Rwork0.223 1374 -
obs--96.39 %

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