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- PDB-4dok: Crystal structure of Arabidopsis thaliana chalcone-isomerase like... -

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Basic information

Entry
Database: PDB / ID: 4dok
TitleCrystal structure of Arabidopsis thaliana chalcone-isomerase like protein At5g05270 (AtCHIL)
ComponentsSimilarity to chalcone-flavonone isomerase
KeywordsISOMERASE / chalcone-isomerase like protein / chalcone-isomerase like fold
Function / homology
Function and homology information


chalcone isomerase / chalcone isomerase activity / flavonoid biosynthetic process
Similarity search - Function
Chalcone--flavonone isomerase 3-like / Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / Chalcone isomerase / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase superfamily / Chalcone isomerase / 10k-s Protein, Hypothetical Protein A; Chain A ...Chalcone--flavonone isomerase 3-like / Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / Chalcone isomerase / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase superfamily / Chalcone isomerase / 10k-s Protein, Hypothetical Protein A; Chain A / 3-Layer(bba) Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Probable chalcone--flavanone isomerase 3 / Probable chalcone--flavanone isomerase 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 1.7 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: Similarity to chalcone-flavonone isomerase
B: Similarity to chalcone-flavonone isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5486
Polymers46,3682
Non-polymers1794
Water6,413356
1
A: Similarity to chalcone-flavonone isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2643
Polymers23,1841
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Similarity to chalcone-flavonone isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2833
Polymers23,1841
Non-polymers992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.997, 65.869, 70.245
Angle α, β, γ (deg.)90.000, 117.150, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-301-

CA

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Components

#1: Protein Similarity to chalcone-flavonone isomerase


Mass: 23184.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g05270 / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9FLC7, UniProt: Q8VZW3*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M sodium TAPS, 28% (w/v) PEG 8000, 0.2 M calcium acetate, 2 mM dithiothreitol, pH 8.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC Quantum Q315 / Detector: CCD / Date: Apr 18, 2008 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 5.9 % / Av σ(I) over netI: 4.3 / Number: 319107 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / D res high: 2.588 Å / D res low: 44.721 Å / Num. obs: 54349 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.2244.7299.310.0460.0467.5
5.818.2210010.0760.0768
4.755.8110010.0850.0858.1
4.114.7510010.0890.0898.2
3.684.1110010.1640.1648
3.363.6810010.260.266.9
3.113.3699.210.3660.3666.3
2.913.1198.510.5720.5724.3
2.742.9198.710.7610.7613.2
2.62.7498.611.2651.2653.1
ReflectionResolution: 1.65→37.222 Å / Num. all: 49989 / Num. obs: 49989 / % possible obs: 88.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.65-1.742.60.4511.51637363850.45177.4
1.74-1.842.60.2892.51558960120.28976.8
1.84-1.972.60.1983.11461155280.19875.6
1.97-2.1330.1461.11897163120.14692
2.13-2.333.10.1031.81863560370.10396.1
2.33-2.613.60.0837.11991055070.08396.6
2.61-3.013.80.0676.71860949340.06797.4
3.01-3.693.50.05281477241770.05298.2
3.69-5.223.70.041131219032530.04198.1
5.22-37.2223.80.03314.2707318440.03398.8

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Phasing

Phasing
Method
SAD
molecular replacement
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.8530.5160.8311.171
2Se600.830.5170.810.823
3Se54.2390.5150.9250.6470.949
4Se600.5460.9260.6381.062
5Se600.7630.9360.571.214
6Se600.6180.8340.8230.93
7Se600.6110.8420.8550.571
8Se10.6930.7280.7870.284
9Se600.6590.8960.6350.678
10Se28.4450.6530.850.990.398
11Se23.6190.6380.8910.5630.382
12Se600.9380.5910.5440.942
13Se600.5810.8410.9740.603
14Se600.7990.7760.8530.758
15Se600.7680.6160.790.484
16Se600.7890.7160.590.685
17Se40.0250.7710.630.7620.482
18Se600.8430.6580.6810.542
19Se600.8070.6370.6260.58
20Se56.8870.7870.5090.6840.524
21Se10.4940.7490.5410.062
22Se10.6040.6840.8560.061
23Se600.7570.9820.7810.672
Phasing MRRfactor: 0.5 / Cor.coef. Fo:Fc: 0.396
Highest resolutionLowest resolution
Rotation3 Å37.22 Å
Translation3 Å37.22 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.21data scaling
MOLREPphasing
SOLVE2.11phasing
CNSrefinement
PDB_EXTRACT3.1data extraction
BOSdata collection
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT / Resolution: 1.7→37.222 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.877 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2341 4.5 %random
Rwork0.1919 ---
obs-46244 89.1 %-
Solvent computationBsol: 37.33 Å2
Displacement parametersBiso max: 51.93 Å2 / Biso mean: 18.6662 Å2 / Biso min: 3.73 Å2
Baniso -1Baniso -2Baniso -3
1--2.856 Å20 Å2-2.01 Å2
2--0.159 Å20 Å2
3---2.697 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3258 0 7 356 3621
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.7372
X-RAY DIFFRACTIONc_scbond_it3.0012.5
X-RAY DIFFRACTIONc_mcangle_it2.5413
X-RAY DIFFRACTIONc_scangle_it4.5544
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 46

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
1.7-1.710.3505400.2925872912872
1.71-1.730.309350.2793761796761
1.73-1.740.3239440.3121843887843
1.74-1.750.2889400.2687858898858
1.75-1.770.2371430.2643795838795
1.77-1.780.2903500.2661828878828
1.78-1.80.2463340.2417817851817
1.8-1.810.2698360.2557822858822
1.81-1.830.3236460.2359800846800
1.83-1.840.2673400.2265847887847
1.84-1.860.2028390.2176773812773
1.86-1.880.3072480.2174826874826
1.88-1.90.1866340.1911806840806
1.9-1.920.2727420.2186788830788
1.92-1.940.2159400.1972838878838
1.94-1.960.2144350.2014809844809
1.96-1.980.2492410.1988789830789
1.98-2.010.2695510.2014850901850
2.01-2.030.232490.1914103610851036
2.03-2.060.3095620.1962102410861024
2.06-2.080.2084550.2096104410991044
2.08-2.110.1764450.1748101210571012
2.11-2.140.1723660.163104011061040
2.14-2.170.1741540.1643101010641010
2.17-2.210.2005600.1761103510951035
2.21-2.240.2028460.1688103410801034
2.24-2.280.1481460.1737104210881042
2.28-2.320.2497470.1846100810551008
2.32-2.370.2815600.1871103210921032
2.37-2.420.2131500.1874103510851035
2.42-2.470.2491640.1941104411081044
2.47-2.530.2228740.20479981072998
2.53-2.590.1818480.1948106411121064
2.59-2.660.2786650.2025103611011036
2.66-2.740.1887570.205101410711014
2.74-2.830.2617630.2056105311161053
2.83-2.930.2386490.2143107111201071
2.93-3.050.2463450.199104510901045
3.05-3.180.2329660.2012105511211055
3.18-3.350.2055580.1928105011081050
3.35-3.560.2039630.1773105511181055
3.56-3.840.1875600.1707102610861026
3.84-4.220.1922630.1521107111341071
4.22-4.830.1898690.1482106211311062
4.83-6.090.2314600.1941107911391079
6.09-500.010.1672590.1976110611651106
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3act.par
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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