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

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Basic information

Entry
Database: PDB / ID: 9etg
TitleCrystal structure of recombinant chicken liver Bile Acid Binding Protein (cL-BABP) in complex with CA-M11
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / fatty acid binding protein / chicken liver bile acid binding protein / recombinant / CA-M11 / bioconjugate
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 Å
AuthorsTassone, G. / Pozzi, C. / Maramai, S.
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

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein, liver
B: Fatty acid-binding protein, liver
C: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7675
Polymers43,5413
Non-polymers1,2262
Water2,936163
1
A: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1262
Polymers14,5141
Non-polymers6131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)14,5141
Polymers14,5141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1262
Polymers14,5141
Non-polymers6131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.563, 60.569, 135.136
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, 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.: 3
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-A1H7S / [4-[(2-azanyl-4-oxidanylidene-1,3-thiazol-5-yl)methyl]phenyl] (4~{R})-4-[(3~{R},5~{R},7~{R},8~{R},9~{S},10~{S},12~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3,7,12-tris(oxidanyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoate


Mass: 612.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H48N2O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M sodium malonate, pH 7.0

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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→135.14 Å / Num. obs: 33892 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.026 / Rrim(I) all: 0.096 / Net I/σ(I): 14.5
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 1.136 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4859 / CC1/2: 0.801 / Rpim(I) all: 0.312 / Rrim(I) all: 1.179

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→67.57 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.036 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28564 1624 4.8 %RANDOM
Rwork0.22189 ---
obs0.22484 32189 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.915 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2→67.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 68 163 3124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123024
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.81.6794112
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9765379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.33223.63135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55615517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5511513
X-RAY DIFFRACTIONr_chiral_restr0.1320.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022207
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_it4.5534.6871522
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.0366.9971899
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.2924.9471502
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.1164.6174345
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 123 -
Rwork0.295 2356 -
obs--100 %

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