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- PDB-5wkr: Crystal structure of chalcone isomerase engineered from ancestral... -

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Basic information

Entry
Database: PDB / ID: 5wkr
TitleCrystal structure of chalcone isomerase engineered from ancestral inference complexed with naringenin (ancCC)
ComponentsEngineered Chalcone Isomerase ancCC
KeywordsISOMERASE / chalcone isomerase / naringenin / flavanone
Function / homology10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / 10k-s Protein, Hypothetical Protein A; Chain A / Chalcone isomerase / 3-Layer(bba) Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta / NARINGENIN
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBurke, J.R. / Kaltenbach, M. / Tawfik, D.S. / Noel, J.P.
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Evolution of chalcone isomerase from a noncatalytic ancestor.
Authors: Kaltenbach, M. / Burke, J.R. / Dindo, M. / Pabis, A. / Munsberg, F.S. / Rabin, A. / Kamerlin, S.C.L. / Noel, J.P. / Tawfik, D.S.
History
DepositionJul 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Engineered Chalcone Isomerase ancCC
B: Engineered Chalcone Isomerase ancCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4747
Polymers47,8942
Non-polymers5805
Water8,179454
1
A: Engineered Chalcone Isomerase ancCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2553
Polymers23,9471
Non-polymers3082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Engineered Chalcone Isomerase ancCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2194
Polymers23,9471
Non-polymers2723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.080, 69.450, 128.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Engineered Chalcone Isomerase ancCC


Mass: 23947.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#2: Chemical ChemComp-NAR / NARINGENIN


Mass: 272.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 42%MPD, 50mM acetic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→33.52 Å / Num. obs: 98865 / % possible obs: 99.8 % / Redundancy: 6.7 % / Net I/σ(I): 11.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DOI

4doi


Resolution: 1.4→33.514 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.96
RfactorNum. reflection% reflection
Rfree0.1673 1998 2.03 %
Rwork0.1372 --
obs0.1378 98653 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→33.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 0 38 454 3724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093643
X-RAY DIFFRACTIONf_angle_d1.265005
X-RAY DIFFRACTIONf_dihedral_angle_d13.8871374
X-RAY DIFFRACTIONf_chiral_restr0.07595
X-RAY DIFFRACTIONf_plane_restr0.007647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4350.33421410.24296821X-RAY DIFFRACTION100
1.435-1.47380.23711420.18796850X-RAY DIFFRACTION100
1.4738-1.51720.18651410.15356873X-RAY DIFFRACTION100
1.5172-1.56610.18721410.13586831X-RAY DIFFRACTION100
1.5661-1.62210.16321420.12826857X-RAY DIFFRACTION100
1.6221-1.68710.16831420.12216869X-RAY DIFFRACTION100
1.6871-1.76380.17231410.12266846X-RAY DIFFRACTION100
1.7638-1.85680.17771430.12166919X-RAY DIFFRACTION100
1.8568-1.97320.18461420.1276864X-RAY DIFFRACTION100
1.9732-2.12550.15151440.12286903X-RAY DIFFRACTION100
2.1255-2.33930.16981440.11726960X-RAY DIFFRACTION100
2.3393-2.67770.16141430.1276966X-RAY DIFFRACTION100
2.6777-3.37310.15271460.14027030X-RAY DIFFRACTION100
3.3731-33.52330.15991460.15117066X-RAY DIFFRACTION97

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