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- PDB-4doi: Crystal structure of Arabidopsis thaliana chalcone isomerase At3g... -

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Basic information

Entry
Database: PDB / ID: 4doi
TitleCrystal structure of Arabidopsis thaliana chalcone isomerase At3g55120 (AtCHI)
ComponentsChalcone--flavonone isomerase 1
KeywordsISOMERASE / chalcone-flavanone isomerase
Function / homology
Function and homology information


response to karrikin / chalcone isomerase / chalcone isomerase activity / extrinsic component of endoplasmic reticulum membrane / plant-type vacuole membrane / flavonoid biosynthetic process / response to auxin / response to UV-B / response to UV / chloroplast ...response to karrikin / chalcone isomerase / chalcone isomerase activity / extrinsic component of endoplasmic reticulum membrane / plant-type vacuole membrane / flavonoid biosynthetic process / response to auxin / response to UV-B / response to UV / chloroplast / endoplasmic reticulum / nucleus / cytosol
Similarity search - Function
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 ...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
NITRATE ION / Chalcone--flavonone isomerase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsNoel, J.P. / Louie, G.V. / Bowman, M.E.
CitationJournal: Nature / Year: 2012
Title: Evolution of the chalcone-isomerase fold from fatty-acid binding to stereospecific catalysis.
Authors: Ngaki, M.N. / Louie, G.V. / Philippe, R.N. / Manning, G. / Pojer, F. / Bowman, M.E. / Li, L. / Larsen, E. / Wurtele, E.S. / Noel, J.P.
History
DepositionFeb 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)53,4956
Polymers53,2472
Non-polymers2484
Water11,710650
1
A: Chalcone--flavonone isomerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7483
Polymers26,6241
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chalcone--flavonone isomerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7483
Polymers26,6241
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.245, 63.781, 80.106
Angle α, β, γ (deg.)90.000, 96.700, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is a monomer

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Components

#1: Protein Chalcone--flavonone isomerase 1 / Chalcone isomerase 1 / Protein TRANSPARENT TESTA 5


Mass: 26623.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g55120, CFI, CHI1, T15C9_120, TT5 / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41088, chalcone isomerase
#2: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M sodium HEPES, 28% (w/v) PEG 8000, 0.3 M magnesium nitrate, 2 mM dithiothreitol, pH 7.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A
DetectorType: ADSC Quantum Q315 / Detector: CCD / Date: Apr 25, 2002 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.55→99 Å / Num. obs: 65875 / % possible obs: 96.1 % / Redundancy: 4.58 % / Rmerge(I) obs: 0.067 / Χ2: 0.731 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.590.4431061.548168.5
1.59-1.630.47437570.935182.6
1.63-1.670.47643160.605195.1
1.67-1.720.42744720.527198.2
1.72-1.770.32245060.491199
1.77-1.840.24645030.484199.1
1.84-1.910.1945340.509199.3
1.91-20.14145380.515199.9
2-2.10.10945440.558199.8
2.1-2.240.08845790.6311100
2.24-2.410.07645510.675199.9
2.41-2.650.06546180.721100
2.65-3.030.05645630.9491100
3.03-3.820.04646091.2231100
3.82-990.03946791.232199.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EYQ

1eyq


Resolution: 1.55→99 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8759 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 3189 4.6 %random
Rwork0.1817 ---
obs-62669 91.3 %-
Solvent computationBsol: 54.2438 Å2
Displacement parametersBiso max: 67.57 Å2 / Biso mean: 21.0736 Å2 / Biso min: 6.47 Å2
Baniso -1Baniso -2Baniso -3
1--3.364 Å20 Å2-0.132 Å2
2--2.198 Å20 Å2
3---1.166 Å2
Refinement stepCycle: LAST / Resolution: 1.55→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 16 650 3975
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5042
X-RAY DIFFRACTIONc_scbond_it2.672.5
X-RAY DIFFRACTIONc_mcangle_it2.2253
X-RAY DIFFRACTIONc_scangle_it4.0384
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.222
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
1.55-1.560.2934400.27570610570
1.56-1.570.2718410.2641768809768
1.57-1.580.313420.2678794836794
1.58-1.590.2574450.282850895850
1.59-1.610.2288630.2514876939876
1.61-1.620.2181410.26249791020979
1.62-1.630.2768520.2829107011221070
1.63-1.640.3392650.2566101910841019
1.64-1.660.2585710.2628111111821111
1.66-1.670.2495570.2504109511521095
1.67-1.680.1836490.2443115412031154
1.68-1.70.212630.2341113712001137
1.7-1.710.3296490.2524116912181169
1.71-1.730.2422680.2363116012281160
1.73-1.750.2421630.2295116812311168
1.75-1.760.2555640.2104120412681204
1.76-1.780.235540.2139115712111157
1.78-1.80.2212690.2148122912981229
1.8-1.820.2251830.203122713101227
1.82-1.840.2565810.2046117012511170
1.84-1.860.236620.1972120312651203
1.86-1.880.1849660.1885123913051239
1.88-1.90.2062770.1827121012871210
1.9-1.930.211680.1957123713051237
1.93-1.950.2284720.1803127713491277
1.95-1.980.1871670.1816126813351268
1.98-2.010.2317650.1753126413291264
2.01-2.040.2119610.1863127113321271
2.04-2.070.1974640.1762127413381274
2.07-2.10.2078800.1737124713271247
2.1-2.140.2188480.1796131713651317
2.14-2.180.1902760.174127213481272
2.18-2.220.1996720.1687129813701298
2.22-2.270.2214730.1775129613691296
2.27-2.320.2345650.1813127313381273
2.32-2.370.2516660.1784130313691303
2.37-2.430.1997640.176129813621298
2.43-2.490.1937590.1518128813471288
2.49-2.570.2002620.1751130213641302
2.57-2.650.2079660.178131613821316
2.65-2.750.2592760.1824126613421266
2.75-2.860.186780.1807129913771299
2.86-2.990.2275660.182130513711305
2.99-3.140.1996780.1879129913771299
3.14-3.340.1875650.1692133013951330
3.34-3.60.1685640.151130413681304
3.6-3.960.1603680.1422132213901322
3.96-4.530.1307700.1404130913791309
4.53-5.710.168650.1733134414091344
5.71-500.010.2035660.1979134214081342
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2no3.par
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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