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

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Basic information

Entry
Database: PDB / ID: 5wks
TitleCrystal structure of chalcone isomerase engineered from ancestral inference complexed with naringenin (ancR1)
ComponentsEngineered Chalcone Isomerase ancR1
KeywordsISOMERASE / chalcone isomerase / naringenin / flavanone
Function / homology
Function and homology information


10k-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
Similarity search - Domain/homology
FORMIC ACID / NARINGENIN
Similarity search - Component
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 ancR1
B: Engineered Chalcone Isomerase ancR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3496
Polymers47,8662
Non-polymers4824
Water9,998555
1
A: Engineered Chalcone Isomerase ancR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2513
Polymers23,9331
Non-polymers3182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Engineered Chalcone Isomerase ancR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0973
Polymers23,9331
Non-polymers1642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.300, 69.120, 126.830
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 ancR1


Mass: 23933.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli K-12 (bacteria)
#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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
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: 1.5→33.34 Å / Num. obs: 79600 / % possible obs: 99.6 % / Redundancy: 9.8 % / Net I/σ(I): 12.8

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Processing

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

4doi


Resolution: 1.5→33.34 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.6
RfactorNum. reflection% reflection
Rfree0.1831 1999 2.51 %
Rwork0.1621 --
obs0.1626 79502 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→33.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 34 555 3813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063516
X-RAY DIFFRACTIONf_angle_d0.9954807
X-RAY DIFFRACTIONf_dihedral_angle_d13.2031310
X-RAY DIFFRACTIONf_chiral_restr0.038567
X-RAY DIFFRACTIONf_plane_restr0.005621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.23951400.19715425X-RAY DIFFRACTION98
1.5375-1.57910.20221400.18795399X-RAY DIFFRACTION99
1.5791-1.62560.20911410.18695465X-RAY DIFFRACTION99
1.6256-1.6780.19171410.17345488X-RAY DIFFRACTION100
1.678-1.7380.20541430.17025503X-RAY DIFFRACTION100
1.738-1.80760.19311420.16715529X-RAY DIFFRACTION100
1.8076-1.88980.22021420.17355510X-RAY DIFFRACTION100
1.8898-1.98950.17711420.16385530X-RAY DIFFRACTION100
1.9895-2.11410.18111430.15985536X-RAY DIFFRACTION100
2.1141-2.27730.18111430.14965572X-RAY DIFFRACTION100
2.2773-2.50640.19511450.16125570X-RAY DIFFRACTION100
2.5064-2.86890.18291450.1635627X-RAY DIFFRACTION100
2.8689-3.61380.17031460.15275663X-RAY DIFFRACTION100
3.6138-33.35240.16921460.15985686X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -3.7138 Å / Origin y: -26.3736 Å / Origin z: 8.5676 Å
111213212223313233
T0.0919 Å20.0093 Å2-0.0011 Å2-0.0817 Å20.0068 Å2--0.1115 Å2
L0.1723 °20.0196 °20.0806 °2-0.0895 °2-0.0365 °2--0.7426 °2
S0.0136 Å °-0.0063 Å °-0.0254 Å °0.0135 Å °0.0016 Å °-0.0013 Å °0.0421 Å °0.0112 Å °0.0016 Å °
Refinement TLS groupSelection details: all

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