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- PDB-5dnv: Crystal structure of KAI2-like protein from Striga (apo state 2) -

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Basic information

Entry
Database: PDB / ID: 5dnv
TitleCrystal structure of KAI2-like protein from Striga (apo state 2)
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 / Hyposensitive to light 3
Similarity search - Component
Biological speciesStriga hermonthica (purple witchweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.65 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 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: ShKAI2iB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5055
Polymers30,2441
Non-polymers2604
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-0 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.000, 76.000, 180.000
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-304-

BEZ

21A-304-

BEZ

31A-304-

BEZ

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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) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3PN85*PLUS
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-BEZ / BENZOIC ACID


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


Mass: 18.015 Da / Num. of mol.: 43 / 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: 50.42 %
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 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→24.88 Å / Num. obs: 9559 / % possible obs: 100 % / Redundancy: 20.2 % / Net I/σ(I): 25
Reflection shellRedundancy: 20.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 5.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 2.65→24.88 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.894 / SU B: 12.833 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 1.292 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26557 485 5.1 %RANDOM
Rwork0.20718 ---
obs0.21017 9057 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.767 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.65→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 0 18 43 2163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192166
X-RAY DIFFRACTIONr_bond_other_d0.0010.022042
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.9472938
X-RAY DIFFRACTIONr_angle_other_deg0.89834668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4115270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08622.85798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71515338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1861517
X-RAY DIFFRACTIONr_chiral_restr0.0640.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212480
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02531
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_it2.1376.4111083
X-RAY DIFFRACTIONr_mcbond_other2.1376.4121084
X-RAY DIFFRACTIONr_mcangle_it3.8369.6061352
X-RAY DIFFRACTIONr_mcangle_other3.8349.6091353
X-RAY DIFFRACTIONr_scbond_it1.6076.6071080
X-RAY DIFFRACTIONr_scbond_other1.6076.6051081
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9119.8231587
X-RAY DIFFRACTIONr_long_range_B_refined6.12750.9942302
X-RAY DIFFRACTIONr_long_range_B_other6.12650.9942303
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 34 -
Rwork0.271 647 -
obs--99.85 %

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