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

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Basic information

Entry
Database: PDB / ID: 9etd
TitleCrystal structure of recombinant chicken liver Bile Acid Binding Protein (cL-BABP) in complex with ursodeoxycholic acid
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / fatty acid binding protein / chicken liver bile acid binding protein / recombinant / bile acid / ursodeoxycholic 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
ISO-URSODEOXYCHOLIC ACID / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)29,8124
Polymers29,0272
Non-polymers7852
Water55831
1
A: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9062
Polymers14,5141
Non-polymers3931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9062
Polymers14,5141
Non-polymers3931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.335, 60.631, 61.672
Angle α, β, γ (deg.)90.00, 95.90, 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-IU5 / ISO-URSODEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.38 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% wt/vol PEG-3500 and 100 mM sodium formate, pH 7.50

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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: 2.3→61.34 Å / Num. obs: 11971 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 58.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.018 / Rrim(I) all: 0.048 / Net I/σ(I): 17.7
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1755 / CC1/2: 0.892 / Rpim(I) all: 0.273 / Rrim(I) all: 0.74 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→61.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.691 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27956 584 4.9 %RANDOM
Rwork0.22043 ---
obs0.22365 11375 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.02 Å2
2--0.1 Å2-0 Å2
3----0.06 Å2
Refine analyzeLuzzati coordinate error free: 0.3821 Å
Refinement stepCycle: 1 / Resolution: 2.3→61.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 56 31 1911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121912
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.6432612
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8065246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.59723.5978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.93515285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.582157
X-RAY DIFFRACTIONr_chiral_restr0.1070.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021391
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_it6.3796.747993
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.96710.0861236
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.3976.662919
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.05890.3232566
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 64 -
Rwork0.351 812 -
obs--100 %

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