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- PDB-4doo: Crystal structure of Arabidopsis thaliana fatty-acid binding prot... -

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Basic information

Entry
Database: PDB / ID: 4doo
TitleCrystal structure of Arabidopsis thaliana fatty-acid binding protein At3g63170 (AtFAP1)
ComponentsChalcone-flavanone isomerase family protein
KeywordsISOMERASE / chalcone-isomerase like fold / fatty-acid binding
Function / homology
Function and homology information


intramolecular lyase activity / chloroplast envelope / plastid / chloroplast stroma / chloroplast / fatty acid metabolic process / fatty acid binding / mitochondrion / cytosol
Similarity search - Function
Chalcone isomerase like / Chalcone isomerase, orthogonal bundle domain superfamily / 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 ...Chalcone isomerase like / Chalcone isomerase, orthogonal bundle domain superfamily / 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
LAURIC ACID / : / Fatty-acid-binding protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsNoel, J.P. / Pojer, F. / 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_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_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-flavanone isomerase family protein
B: Chalcone-flavanone isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3958
Polymers45,5162
Non-polymers8796
Water8,467470
1
A: Chalcone-flavanone isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1984
Polymers22,7581
Non-polymers4403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chalcone-flavanone isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1984
Polymers22,7581
Non-polymers4403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.489, 56.901, 139.608
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chalcone-flavanone isomerase family protein / Putative uncharacterized protein At3g63170 / Putative uncharacterized protein At3g63170 / F16M2_20 ...Putative uncharacterized protein At3g63170 / Putative uncharacterized protein At3g63170 / F16M2_20 / Putative uncharacterized protein F16M2_20


Mass: 22757.826 Da / Num. of mol.: 2 / Fragment: unp residues 74-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g63170, At3g63170/F16M2_20, F16M2_20 / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9M1X2
#2: Chemical
ChemComp-DAO / LAURIC ACID / Lauric acid


Mass: 200.318 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H24O2
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M sodium TAPS, 19% (w/v) PEG 3350, 0.3 M potassium chloride, 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: SSRL / Beamline: BL9-2 / Wavelength: 1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 1, 2002 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 36084

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→100 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8399 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 1799 5 %random
Rwork0.1996 ---
obs-36084 99.4 %-
Solvent computationBsol: 44.3444 Å2
Displacement parametersBiso max: 66.85 Å2 / Biso mean: 24.8433 Å2 / Biso min: 7.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.198 Å20 Å20 Å2
2---0.116 Å20 Å2
3----0.082 Å2
Refinement stepCycle: LAST / Resolution: 1.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3172 0 58 470 3700
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.0032
X-RAY DIFFRACTIONc_scbond_it3.2942.5
X-RAY DIFFRACTIONc_mcangle_it2.8143
X-RAY DIFFRACTIONc_scangle_it4.9934
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.205
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 35

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
1.9-1.920.2642450.2055933978933
1.92-1.940.2516430.20119741017974
1.94-1.960.2589460.21659901036990
1.96-1.980.261560.2101928984928
1.98-20.27550.2089631018963
2-2.020.2901520.21269821034982
2.02-2.050.3418500.22169631013963
2.05-2.070.2491430.21239721015972
2.07-2.10.2143410.20049871028987
2.1-2.130.233430.21179581001958
2.13-2.150.2568490.20069751024975
2.15-2.190.281570.20119831040983
2.19-2.220.2262540.19839671021967
2.22-2.250.2503420.18439731015973
2.25-2.290.2245440.20899841028984
2.29-2.330.2743480.19369531001953
2.33-2.370.2317380.208101510531015
2.37-2.420.2762450.20889561001956
2.42-2.470.2834480.2133100110491001
2.47-2.520.2472500.21779621012962
2.52-2.580.2864630.2139891052989
2.58-2.640.3391520.23219581010958
2.64-2.710.1988500.20139831033983
2.71-2.790.3012580.21959711029971
2.79-2.880.2861570.21929751032975
2.88-2.990.3411440.2251100910531009
2.99-3.110.2667540.22079681022968
3.11-3.250.2544550.22029811036981
3.25-3.420.2549540.20529961050996
3.42-3.630.2603680.18419791047979
3.63-3.920.221670.17959671034967
3.92-4.310.1859550.16959991054999
4.31-4.930.206660.16499981064998
4.93-6.220.2664670.2041103010971060
6.22-500.010.1917400.1786106311031063
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4C12.par

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