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- PDB-5l8o: crystal structure of human FABP6 in complex with cholate -

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Basic information

Entry
Database: PDB / ID: 5l8o
Titlecrystal structure of human FABP6 in complex with cholate
ComponentsGastrotropin
KeywordsLIPID BINDING PROTEIN / FABP6 / Fatty acid binding protein 6 / Ileal bile acid binding protein / I-BABP / Ileal / Gastrotropin / Fragments / cholate
Function / homology
Function and homology information


NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Triglyceride catabolism / fatty acid transport / Recycling of bile acids and salts / fatty acid binding / lipid metabolic process / negative regulation of cell population proliferation / lipid binding / membrane / nucleus ...NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Triglyceride catabolism / fatty acid transport / Recycling of bile acids and salts / fatty acid binding / lipid metabolic process / negative regulation of cell population proliferation / lipid binding / membrane / nucleus / cytoplasm / 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 beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CHOLIC ACID / DI(HYDROXYETHYL)ETHER / Gastrotropin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsHendrick, A. / Mueller, I. / Leonard, P.M. / Davenport, R. / Mitchell, P.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Identification and Investigation of Novel Binding Fragments in the Fatty Acid Binding Protein 6 (FABP6).
Authors: Hendrick, A.G. / Muller, I. / Willems, H. / Leonard, P.M. / Irving, S. / Davenport, R. / Ito, T. / Reeves, J. / Wright, S. / Allen, V. / Wilkinson, S. / Heffron, H. / Bazin, R. / Turney, J. / Mitchell, P.J.
History
DepositionJun 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: Gastrotropin
B: Gastrotropin
C: Gastrotropin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7896
Polymers43,1683
Non-polymers6213
Water81145
1
A: Gastrotropin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4952
Polymers14,3891
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gastrotropin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9043
Polymers14,3891
Non-polymers5152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Gastrotropin


Theoretical massNumber of molelcules
Total (without water)14,3891
Polymers14,3891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.860, 64.720, 59.330
Angle α, β, γ (deg.)90.00, 94.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gastrotropin / GT / Fatty acid-binding protein 6 / Ileal lipid-binding protein / ILBP / Intestinal 15 kDa protein ...GT / Fatty acid-binding protein 6 / Ileal lipid-binding protein / ILBP / Intestinal 15 kDa protein / I-15P / Intestinal bile acid-binding protein / I-BABP


Mass: 14389.235 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP6, ILBP, ILLBP / Production host: Escherichia coli (E. coli) / References: UniProt: P51161
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 41% w/v PEG 3350 and 0.1 M Bis-tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.39→59.18 Å / Num. obs: 14115 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 12
Reflection shellResolution: 2.39→2.45 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3elx

3elx


Resolution: 2.39→59.18 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 11.71 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R: 0.679 / ESU R Free: 0.318 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28139 731 5.2 %RANDOM
Rwork0.22614 ---
obs0.22896 13374 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.159 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-1.5 Å2
2---1.02 Å2-0 Å2
3---1.5 Å2
Refinement stepCycle: 1 / Resolution: 2.39→59.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 43 45 2871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192874
X-RAY DIFFRACTIONr_bond_other_d0.0010.022606
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.9393886
X-RAY DIFFRACTIONr_angle_other_deg0.80935957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1585368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52824.878123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42315450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.497159
X-RAY DIFFRACTIONr_chiral_restr0.0690.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02678
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_it1.7515.4671484
X-RAY DIFFRACTIONr_mcbond_other1.7515.4671483
X-RAY DIFFRACTIONr_mcangle_it3.128.21848
X-RAY DIFFRACTIONr_mcangle_other3.1198.21849
X-RAY DIFFRACTIONr_scbond_it1.525.531390
X-RAY DIFFRACTIONr_scbond_other1.525.531390
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6498.2332039
X-RAY DIFFRACTIONr_long_range_B_refined4.73942.3732846
X-RAY DIFFRACTIONr_long_range_B_other4.73942.3792847
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 53 -
Rwork0.27 985 -
obs--99.9 %

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