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- PDB-6cjn: Crystal Structure of Chalcone Isomerase from Medicago Sativa with... -

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Basic information

Entry
Database: PDB / ID: 6cjn
TitleCrystal Structure of Chalcone Isomerase from Medicago Sativa with the G95T mutation
ComponentsChalcone--flavonone isomerase 1
Keywordsplant protein / isomerase / chalcone isomerase / naringenin / flavanone
Function / homology
Function and homology information


chalcone isomerase / chalcone isomerase activity / flavonoid biosynthetic process
Similarity search - Function
Chalcone--flavonone isomerase / Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase / Chalcone isomerase superfamily / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / Chalcone isomerase / 10k-s Protein, Hypothetical Protein A; Chain A ...Chalcone--flavonone isomerase / Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase / Chalcone isomerase superfamily / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / Chalcone isomerase / 10k-s Protein, Hypothetical Protein A; Chain A / 3-Layer(bba) Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chalcone--flavanone isomerase 1
Similarity search - Component
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBurke, J.R. / La Clair, J.J. / Philippe, R.N. / Pabis, A. / Jez, J.M. / Cortina, G. / Kaltenbach, M. / Bowman, M.E. / Woods, K.B. / Nelson, A.T. ...Burke, J.R. / La Clair, J.J. / Philippe, R.N. / Pabis, A. / Jez, J.M. / Cortina, G. / Kaltenbach, M. / Bowman, M.E. / Woods, K.B. / Nelson, A.T. / Tawfik, D.S. / Kamerlin, S.C.L. / Noel, J.P.
CitationJournal: Acs Catalysis / Year: 2019
Title: Bifunctional Substrate Activation via an Arginine Residue Drives Catalysis in Chalcone Isomerases
Authors: Burke, J.R. / La Clair, J.J. / Philippe, R.N. / Pabis, A. / Jez, J.M. / Cortina, G. / Kaltenbach, M. / Bowman, M.E. / Woods, K.B. / Nelson, A.T. / Tawfik, D.S. / Kamerlin, S.C.L. / Noel, J.P.
History
DepositionFeb 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 13, 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: Chalcone--flavonone isomerase 1
B: Chalcone--flavonone isomerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9328
Polymers48,3552
Non-polymers5766
Water1,40578
1
A: Chalcone--flavonone isomerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4664
Polymers24,1781
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chalcone--flavonone isomerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4664
Polymers24,1781
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.820, 90.820, 352.423
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-428-

HOH

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Components

#1: Protein Chalcone--flavonone isomerase 1 / Chalcone isomerase 1


Mass: 24177.566 Da / Num. of mol.: 2 / Mutation: G95T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / Gene: CHI1, CHI-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P28012, chalcone isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 4.34 Å3/Da / Density % sol: 71.65 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: crystals grew over 1 week at 20mgs/ml in 2.2M AmSO4, 50mM hepes pH 7.5 and 25% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.4→88.11 Å / Num. obs: 34785 / % possible obs: 99.9 % / Redundancy: 12.1 % / Net I/σ(I): 7.1
Reflection shellResolution: 2.4→2.46 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→76.764 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.22
RfactorNum. reflection% reflection
Rfree0.2403 1999 5.75 %
Rwork0.2108 --
obs0.2125 34785 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→76.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 30 78 3426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033408
X-RAY DIFFRACTIONf_angle_d0.7574616
X-RAY DIFFRACTIONf_dihedral_angle_d12.2871246
X-RAY DIFFRACTIONf_chiral_restr0.03522
X-RAY DIFFRACTIONf_plane_restr0.004590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.33321380.30992278X-RAY DIFFRACTION100
2.46-2.52660.3711400.30962281X-RAY DIFFRACTION100
2.5266-2.60090.35521380.29082269X-RAY DIFFRACTION100
2.6009-2.68490.31951390.28322294X-RAY DIFFRACTION100
2.6849-2.78080.32031400.27312276X-RAY DIFFRACTION100
2.7808-2.89220.33261400.26412308X-RAY DIFFRACTION100
2.8922-3.02380.29661420.24372332X-RAY DIFFRACTION100
3.0238-3.18320.27831400.24482295X-RAY DIFFRACTION100
3.1832-3.38270.27241430.23232343X-RAY DIFFRACTION100
3.3827-3.64380.25061430.22222346X-RAY DIFFRACTION100
3.6438-4.01050.20281430.18712346X-RAY DIFFRACTION100
4.0105-4.59080.19951460.17692387X-RAY DIFFRACTION100
4.5908-5.78360.20531490.1712435X-RAY DIFFRACTION100
5.7836-76.80320.19041580.17762596X-RAY DIFFRACTION99

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