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

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Basic information

Entry
Database: PDB / ID: 4dol
TitleCrystal structure of Arabidopsis thaliana fatty-acid binding protein At1g53520 (AtFAP3)
ComponentsAt1g53520
KeywordsISOMERASE / chalcone-isomerase like fold / fatty-acid binding
Function / homology
Function and homology information


intramolecular lyase activity / chloroplast stroma / fatty acid metabolic process / chloroplast / fatty acid binding
Similarity search - Function
Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / Chalcone isomerase, 3-layer sandwich / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / Chalcone isomerase / Chalcone isomerase superfamily / 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 / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / Chalcone isomerase / 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
PALMITIC ACID / Fatty-acid-binding protein 3, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.2Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: At1g53520
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3852
Polymers23,1291
Non-polymers2561
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.908, 52.911, 95.563
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 At1g53520 / Chalcone isomerase / putative / 94270-95700 / Chalcone isomerase-like protein


Mass: 23129.037 Da / Num. of mol.: 1 / Fragment: unp residues 71-287 / Mutation: R140C, G141C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g53520, F22G10.11 / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9C8L2
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium PIPES, 8% (w/v) PEG 8000, 0.2 M calcium acetate, 2 mM dithiothreitol, pH 6.5, 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: Jul 11, 2008 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→46.274 Å / Num. all: 29609 / Num. obs: 29609 / % possible obs: 99.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 20.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.795.60.5751.32363442230.57599.3
1.79-1.97.10.3382.22875840550.338100
1.9-2.037.10.1544.82689038020.154100
2.03-2.197.10.0937.62508535560.093100
2.19-2.470.0689.52307432870.068100
2.4-2.696.90.05610.82071229840.056100
2.69-3.16.90.04413.11834026730.044100
3.1-3.86.70.04113.31502022580.041100
3.8-5.386.20.03417.51102917930.03499.9
5.38-46.2746.30.02623.261949780.02693.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.574 / Cor.coef. Fo:Fc: 0.189
Highest resolutionLowest resolution
Rotation3 Å45.61 Å
Translation3 Å45.61 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.21data scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DOI

4doi


Resolution: 1.7→46.274 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8552 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 1503 5.1 %random
Rwork0.2029 ---
obs-29551 99.6 %-
Solvent computationBsol: 58.7178 Å2
Displacement parametersBiso max: 76.33 Å2 / Biso mean: 35.2456 Å2 / Biso min: 9.22 Å2
Baniso -1Baniso -2Baniso -3
1-3.544 Å20 Å20 Å2
2---6.013 Å20 Å2
3---2.469 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 18 197 1779
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.1882.5
X-RAY DIFFRACTIONc_scbond_it3.4453.5
X-RAY DIFFRACTIONc_mcangle_it3.1954
X-RAY DIFFRACTIONc_scangle_it5.1265
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.147
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
1.7-1.720.3952460.365890936890
1.72-1.740.4375550.3498923978923
1.74-1.760.3837550.3197910965910
1.76-1.780.4203450.2985938983938
1.78-1.810.3493530.2947908961908
1.81-1.830.3258410.2943928969928
1.83-1.860.3105540.2728926980926
1.86-1.890.3044450.2633927972927
1.89-1.910.2491540.2493919973919
1.91-1.950.2496490.2232931980931
1.95-1.980.2379520.2256916968916
1.98-2.020.2542380.201944982944
2.02-2.050.2365490.2184933982933
2.05-2.10.2288450.228926971926
2.1-2.140.2704510.2172929980929
2.14-2.190.2793480.2152935983935
2.19-2.250.2093550.1993931986931
2.25-2.310.2587510.2086933984933
2.31-2.380.2157600.2159924984924
2.38-2.450.1708450.1928932977932
2.45-2.540.2299640.20969381002938
2.54-2.640.3311420.2053952994952
2.64-2.760.2208470.1904937984937
2.76-2.910.2598500.2217941991941
2.91-3.090.2461460.20829721018972
3.09-3.330.2564620.2163925987925
3.33-3.660.1983580.19259531011953
3.66-4.190.1424490.16079701019970
4.19-5.280.1264480.16059901038990
5.28-500.010.2195460.20919671013967
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3plm.par

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