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- PDB-8b7r: Bacterial chalcone isomerase with taxifolin chalcone -

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Basic information

Entry
Database: PDB / ID: 8b7r
TitleBacterial chalcone isomerase with taxifolin chalcone
ComponentsChalcone isomerase
KeywordsISOMERASE / BACTERIAL CHALCONE ISOMERASE / FLAVONOIDS / Taxifoline chalcone
Function / homologyChalcone isomerase, N-terminal / Chalcone isomerase N-terminal domain / chalcone isomerase / chalcone isomerase activity / : / Chem-Q0X / Chalcone isomerase
Function and homology information
Biological speciesEubacterium ramulus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHinrichs, W. / Palm, G.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Molecules / Year: 2022
Title: Structural Basis for (2 R ,3 R )-Taxifolin Binding and Reaction Products to the Bacterial Chalcone Isomerase of Eubacterium ramulus .
Authors: Palm, G.J. / Thomsen, M. / Berndt, L. / Hinrichs, W.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2015
Title: Structure and catalytic mechanism of the evolutionarily unique bacterial chalcone isomerase.
Authors: Thomsen, M. / Tuukkanen, A. / Dickerhoff, J. / Palm, G.J. / Kratzat, H. / Svergun, D.I. / Weisz, K. / Bornscheuer, U.T. / Hinrichs, W.
History
DepositionOct 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 11, 2023Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_assembly_prop
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chalcone isomerase
B: Chalcone isomerase
C: Chalcone isomerase
D: Chalcone isomerase
E: Chalcone isomerase
F: Chalcone isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,09241
Polymers195,2286
Non-polymers2,86535
Water32,3911798
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31940 Å2
ΔGint-329 kcal/mol
Surface area51810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.823, 193.154, 205.288
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-678-

HOH

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Components

#1: Protein
Chalcone isomerase / / Taxifolin isomerase


Mass: 32537.928 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium ramulus (bacteria) / Gene: tai / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: V9P0A9, chalcone isomerase
#2: Chemical
ChemComp-Q0X / (Z)-3-[3,4-bis(oxidanyl)phenyl]-2-oxidanyl-1-[2,4,6-tris(oxidanyl)phenyl]prop-2-en-1-one / taxifolin chalcone


Mass: 304.252 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C15H12O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1798 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.46 Å3/Da / Density % sol: 72.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 6.8 mg/ml CHI 50 mM Na phosphate, pH 6.8. Precipitant 1.8 M (NH4)2SO4, 0.2 M NaCl, 0.1 M HEPES pH 7.5. Soaking for 10 min in 2.5 mM taxifolin (2.5% ethanol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.13→48.82 Å / Num. obs: 191642 / % possible obs: 99.5 % / Redundancy: 7.56 % / Biso Wilson estimate: 36.5 Å2 / CC1/2: 1 / Rrim(I) all: 0.188 / Net I/σ(I): 10.74
Reflection shellResolution: 2.13→2.25 Å / Redundancy: 7.56 % / Mean I/σ(I) obs: 1.93 / Num. unique obs: 30350 / CC1/2: 0.33 / Rrim(I) all: 1.1 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D06

4d06


Resolution: 2.15→48.29 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 7.957 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1897 2035 1.1 %RANDOM
Rwork0.1632 ---
obs0.1635 183628 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 190.85 Å2 / Biso mean: 35.332 Å2 / Biso min: 20.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0 Å20 Å2
2---0.92 Å20 Å2
3---1.09 Å2
Refinement stepCycle: final / Resolution: 2.15→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12794 0 161 1801 14756
Biso mean--98.88 42.5 -
Num. residues----1559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01213476
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611922
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.65618365
X-RAY DIFFRACTIONr_angle_other_deg0.5041.56327827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.73151581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.186566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.947102157
X-RAY DIFFRACTIONr_chiral_restr0.0740.21841
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215231
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022893
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 149 -
Rwork0.335 13448 -
all-13597 -
obs--99.65 %
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)
10.2707-0.0982-0.0040.14340.0280.22780.0327-0.00060.0144-0.0248-0.03730.0094-0.00620.08690.00460.2459-0.0310.00430.36450.0180.021654.38275.53966.846
20.0818-0.01730.03340.27420.00120.21740.0302-0.03080.00630.0264-0.0423-0.0185-0.0380.01860.01210.3051-0.0760.00080.3187-0.01960.012134.25692.2985.838
30.1956-0.0241-0.13470.1919-0.12930.38080.04040.0245-0.0408-0.0551-0.03110.0170.0221-0.0142-0.00930.3219-0.0262-0.03510.2969-0.02970.018123.08361.02445.72
40.53740.1083-0.03090.11760.08290.12780.02270.00380.041-0.0191-0.00590.04170.00890.0021-0.01690.2746-0.0356-0.01380.29190.01270.06713.00778.75163.869
50.21380.1396-0.06140.37850.12490.15150.0655-0.037-0.06720.0432-0.0397-0.05260.03060.031-0.02570.2962-0.016-0.07220.2710.02980.071436.37241.30778.579
60.1728-0.0631-0.03720.09820.07770.40430.0702-0.0842-0.0101-0.0025-0.03440.00720.0578-0.0434-0.03580.2948-0.1297-0.02240.35310.03080.008815.50758.15996.535
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 282
2X-RAY DIFFRACTION2B1 - 282
3X-RAY DIFFRACTION3C1 - 282
4X-RAY DIFFRACTION4D1 - 282
5X-RAY DIFFRACTION5E1 - 282
6X-RAY DIFFRACTION6F1 - 282

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