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- PDB-5l8i: crystal structure of human FABP6 apo-protein -

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Basic information

Entry
Database: PDB / ID: 5l8i
Titlecrystal structure of human FABP6 apo-protein
ComponentsGastrotropin
KeywordsSIGNALING PROTEIN / FABP6 / Fatty acid binding protein 6 / Ileal bile acid binding protein / I-BABP / Ileal / Gastrotropin / Fragments
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 / cytosol / cytoplasm
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Gastrotropin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)43,9457
Polymers43,1683
Non-polymers7774
Water1,06359
1
A: Gastrotropin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5392
Polymers14,3891
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gastrotropin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0164
Polymers14,3891
Non-polymers6273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Gastrotropin


Theoretical massNumber of molelcules
Total (without water)14,3891
Polymers14,3891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.952, 64.114, 58.765
Angle α, β, γ (deg.)90.00, 94.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ABC

#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

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Non-polymers , 5 types, 63 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.04 Å3/Da / Density % sol: 39.78 %
Crystal growTemperature: 293.5 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: 0.97623 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: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.88→58.58 Å / Num. obs: 28093 / % possible obs: 99 % / Redundancy: 3.2 % / Biso Wilson estimate: 34.5 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.081 / Net I/σ(I): 5.5
Reflection shellResolution: 1.88→1.96 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 1.5 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3exl

3exl


Resolution: 1.88→58.58 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.919 / SU B: 12.462 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.175 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27513 1365 4.9 %RANDOM
Rwork0.23968 ---
obs0.2415 26690 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.573 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.56 Å2
2---0.31 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.88→58.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 52 59 2928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192913
X-RAY DIFFRACTIONr_bond_other_d0.0020.022652
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9353916
X-RAY DIFFRACTIONr_angle_other_deg0.90736071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7865373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.60925126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22915459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.321159
X-RAY DIFFRACTIONr_chiral_restr0.0890.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023342
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
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_it1.1232.3531501
X-RAY DIFFRACTIONr_mcbond_other1.1222.3531500
X-RAY DIFFRACTIONr_mcangle_it1.9623.5261871
X-RAY DIFFRACTIONr_mcangle_other1.9613.5261872
X-RAY DIFFRACTIONr_scbond_it1.2432.511412
X-RAY DIFFRACTIONr_scbond_other1.2432.5121413
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0593.6672046
X-RAY DIFFRACTIONr_long_range_B_refined5.10821.8711225
X-RAY DIFFRACTIONr_long_range_B_other5.10821.87311226
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 84 -
Rwork0.387 1874 -
obs--94.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3514-1.15290.69981.4241-0.06620.71690.07420.3614-0.308-0.1065-0.03860.23690.0908-0.0262-0.03560.033-0.0136-0.02540.049-0.02420.082548.905-7.95359.214
22.9566-1.63421.76293.7077-0.86062.619-0.253-0.3897-0.05210.57570.2546-0.0536-0.1558-0.1672-0.00160.10230.0411-0.01290.08320.0190.011167.5111.77175.539
30.94090.86181.45642.75952.95536.2301-0.12360.23440.0923-0.42010.1949-0.0732-0.31420.7842-0.07120.19690.01220.0170.33330.04750.060437.896-8.42592.154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 127
2X-RAY DIFFRACTION2B2 - 127
3X-RAY DIFFRACTION3C3 - 127

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