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- PDB-7o0j: High resolution structure of recombinant chichen liver Bile Acid ... -

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Basic information

Entry
Database: PDB / ID: 7o0j
TitleHigh resolution structure of recombinant chichen liver Bile Acid Binding Protein (cL-BABP)
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / fatty acid binding protein / chicken liver bile acid binding protein / recombinant
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 / Lipocalin / cytosolic fatty-acid binding protein family / Calycin
Similarity search - Domain/homology
Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTassone, G. / Pozzi, C.
CitationJournal: Biomolecules / Year: 2021
Title: Validation of Recombinant Chicken Liver Bile Acid Binding Protein as a Tool for Cholic Acid Hosting.
Authors: Tassone, G. / Orlandini, M. / Olivucci, M. / Pozzi, C.
History
DepositionMar 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)14,5141
Polymers14,5141
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.014, 58.931, 71.288
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 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.: 1
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) / Variant (production host): BL21(DE3)GOLD / References: UniProt: P80226
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 % vol/vol 2-propanol, 20 % PEG4000 and 100 mM Hepes, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.892 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 4, 2019
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.892 Å / Relative weight: 1
ReflectionResolution: 1.4→71.29 Å / Num. obs: 32871 / % possible obs: 99.3 % / Redundancy: 9.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.013 / Rrim(I) all: 0.04 / Net I/σ(I): 24.3
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 4682 / CC1/2: 0.864 / Rpim(I) all: 0.225 / Rrim(I) all: 0.688 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TVQ

1tvq


Resolution: 1.4→32.55 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.948 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 1657 5 %RANDOM
Rwork0.158 ---
obs0.1604 31165 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 292.04 Å2 / Biso mean: 30.033 Å2 / Biso min: 13.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å2-0 Å20 Å2
2---0.26 Å2-0 Å2
3----0.31 Å2
Refine analyzeLuzzati coordinate error obs: 0.2001 Å
Refinement stepCycle: final / Resolution: 1.4→32.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 0 213 1191
Biso mean---43.59 -
Num. residues----126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0121073
X-RAY DIFFRACTIONr_angle_refined_deg2.6191.6581464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06922.90955
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11215209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.728157
X-RAY DIFFRACTIONr_chiral_restr0.1640.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.02814
X-RAY DIFFRACTIONr_rigid_bond_restr16.2333925
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 111 -
Rwork0.247 2238 -
all-2349 -
obs--98.12 %

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