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- PDB-9dxi: Crystal structure of dimer Caenorhabditis elegans lipid binding p... -

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Basic information

Entry
Database: PDB / ID: 9dxi
TitleCrystal structure of dimer Caenorhabditis elegans lipid binding protein 3 (LBP-3)
ComponentsFatty acid-binding protein homolog 3
KeywordsLIPID BINDING PROTEIN / LBP3 / LBP-3 / FABP / fatty acid binding protein lipid / lipid binding protein 3 / lysosome / aging / Caenorhabditis elegans / lipid transport / polyunsaturated fatty acids
Function / homologyFatty acid-binding protein homologue 1/2/3/4 / Cytosolic fatty-acid binding proteins signature. / Cytosolic fatty-acid binding / Calycin / lipid binding / extracellular region / Fatty acid-binding protein homolog 3
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsCuevas, A.R. / Tillman, M.C. / Ortlund, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: Protein Sci. / Year: 2025
Title: Structural dynamics and binding of Caenorhabditis elegans lifespan-extending lipid binding protein-3 to polyunsaturated fatty acids.
Authors: Cuevas, A.R. / Tillman, M.C. / Wang, M.C. / Ortlund, E.A.
History
DepositionOct 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein homolog 3
B: Fatty acid-binding protein homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9643
Polymers34,8722
Non-polymers921
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-17 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.731, 68.846, 103.891
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fatty acid-binding protein homolog 3 / Lipid-binding protein 3


Mass: 17435.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lbp-3, F40F4.4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q20222
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 14% PEG 3350, 0.16 M NaCl, 0.1 M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 17848 / % possible obs: 99.7 % / Redundancy: 10.1 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.065 / Rrim(I) all: 0.212 / Χ2: 1.519 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.17-2.266.71.3117050.6340.8810.5281.4170.55698.9
2.26-2.358.51.37917540.9330.9820.4891.4650.49199.9
2.35-2.469.21.03717570.9310.9820.3541.0970.57499.8
2.46-2.5810.51.08317750.9440.9860.3421.1370.61199.9
2.58-2.7511.50.99917590.9750.9940.3021.0440.72199.9
2.75-2.9611.70.69417760.980.9950.2090.7260.9199.9
2.96-3.2610.80.43117760.980.9950.1370.4531.32999.4
3.26-3.7312.20.23517940.9910.9980.0710.2462.02999.9
3.73-4.711.20.12418230.9960.9990.040.1312.82999.9
4.7-508.70.10219290.9960.9990.0380.1094.67999.1

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→38.09 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 885 4.99 %
Rwork0.2194 --
obs0.2219 17721 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→38.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 6 59 2351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032392
X-RAY DIFFRACTIONf_angle_d0.5743215
X-RAY DIFFRACTIONf_dihedral_angle_d16.875886
X-RAY DIFFRACTIONf_chiral_restr0.043333
X-RAY DIFFRACTIONf_plane_restr0.005409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.310.31621390.26242660X-RAY DIFFRACTION96
2.31-2.490.33441450.26182750X-RAY DIFFRACTION99
2.49-2.740.30581460.26452792X-RAY DIFFRACTION99
2.74-3.130.29761480.26032809X-RAY DIFFRACTION100
3.13-3.940.25211510.20962858X-RAY DIFFRACTION100
3.95-38.090.25011560.19582967X-RAY DIFFRACTION99

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