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- PDB-9ete: Crystal structure of recombinant chicken liver Bile Acid Binding ... -

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Basic information

Entry
Database: PDB / ID: 9ete
TitleCrystal structure of recombinant chicken liver Bile Acid Binding Protein (cL-BABP) in complex with deoxycholic acid
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / fatty acid binding protein / chicken liver bile acid binding protein / recombinant / bile acid / deoxycholic acid
Function / homology
Function and homology information


fatty acid transport / fatty acid binding / nucleus / cytosol
Similarity search - Function
Lipocalin / cytosolic fatty-acid binding protein family / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin
Similarity search - Domain/homology
Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTassone, G. / Pozzi, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2024
Title: Exploiting the bile acid binding protein as transporter of a Cholic Acid/Mirin bioconjugate for potential applications in liver cancer therapy.
Authors: Tassone, G. / Maramai, S. / Paolino, M. / Lamponi, S. / Poggialini, F. / Dreassi, E. / Petricci, E. / Alcaro, S. / Pozzi, C. / Romeo, I.
History
DepositionMar 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: 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, liver
B: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5986
Polymers29,0272
Non-polymers1,5704
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.516, 60.375, 64.105
Angle α, β, γ (deg.)90.00, 99.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fatty acid-binding protein, liver / Fatty acid-binding protein 1 / Liver basic FABP / LB-FABP / Liver bile acid-binding protein / L- ...Fatty acid-binding protein 1 / Liver basic FABP / LB-FABP / Liver bile acid-binding protein / L-BABP / Liver-type fatty acid-binding protein / L-FABP


Mass: 14513.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: FABP1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P80226
#2: Chemical
ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H40O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.4 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% wt/vol PEG-3500, 200 mM lithium sulfate monohydrate, and 100 mM BIS-TRIS, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 13, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→63.28 Å / Num. obs: 13482 / % possible obs: 83.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 26.5 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.076 / Rrim(I) all: 0.128 / Net I/σ(I): 5.1
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2018 / CC1/2: 0.857 / Rpim(I) all: 0.262 / Rrim(I) all: 0.444

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→36.07 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.85 / SU B: 11.079 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R: 0.421 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.34657 679 5 %RANDOM
Rwork0.24169 ---
obs0.24716 12801 83.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.625 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.02 Å2
2---0 Å20 Å2
3---0.02 Å2
Refine analyzeLuzzati coordinate error free: 0.3226 Å
Refinement stepCycle: 1 / Resolution: 2.1→36.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1887 0 112 236 2235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122047
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.642799
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0815246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77523.26192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.2615336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9771510
X-RAY DIFFRACTIONr_chiral_restr0.1070.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021446
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9513.331990
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.2854.9661234
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3553.4961057
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.81646.853013
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 55 -
Rwork0.303 991 -
obs--85.74 %

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