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- PDB-3elx: Crystal structure of apo Zebrafish Ileal Bile Acid-Binding Protein -

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Basic information

Entry
Database: PDB / ID: 3elx
TitleCrystal structure of apo Zebrafish Ileal Bile Acid-Binding Protein
ComponentsIleal bile acid-binding protein
KeywordsLIPID BINDING PROTEIN / ileal bile acid-bindign protein / zebrafish / cholic acid / Lipid-binding / Transport
Function / homology
Function and homology information


Recycling of bile acids and salts / Triglyceride catabolism / bile acid binding / fatty acid transport / fatty acid binding / membrane / nucleus / cytosol
Similarity search - Function
Lipocalin / cytosolic fatty-acid binding protein family / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCapaldi, S. / Saccomani, G. / Fessas, D. / Signorelli, M. / Perduca, M. / Monaco, H.L.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The X-Ray structure of zebrafish (Danio rerio) ileal bile acid-binding protein reveals the presence of binding sites on the surface of the protein molecule.
Authors: Capaldi, S. / Saccomani, G. / Fessas, D. / Signorelli, M. / Perduca, M. / Monaco, H.L.
History
DepositionSep 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ileal bile acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2532
Polymers15,1911
Non-polymers621
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.422, 54.422, 82.696
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological unit is the monomer.

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Components

#1: Protein Ileal bile acid-binding protein / Fatty acid binding protein 6 / ileal (Gastrotropin)


Mass: 15191.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: fabp6, zgc:92421 / Plasmid: pQE50 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q6IMW5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Sodium HEPES, 1.4 M tri-sodium citrate dihydrate, 1% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2007 / Details: toroidal mirror
RadiationMonochromator: Si 311 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.6→41 Å / Num. all: 18986 / Num. obs: 18986 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 16.9
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 6.4 / Num. unique all: 2731 / Rsym value: 0.281 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QO4

2qo4


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.193 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.098 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 977 5.1 %RANDOM
Rwork0.20246 ---
all0.20433 18978 --
obs0.20433 18001 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.547 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 4 133 1167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221052
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.9531416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3815133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.1425.81443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94115189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.374152
X-RAY DIFFRACTIONr_chiral_restr0.0760.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02773
X-RAY DIFFRACTIONr_nbd_refined0.1870.2405
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2708
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2106
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.218
X-RAY DIFFRACTIONr_mcbond_it0.8551.5674
X-RAY DIFFRACTIONr_mcangle_it1.27421062
X-RAY DIFFRACTIONr_scbond_it2.0883428
X-RAY DIFFRACTIONr_scangle_it3.2534.5354
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 69 -
Rwork0.217 1292 -
obs-1361 99.93 %
Refinement TLS params.Method: refined / Origin x: 27.3197 Å / Origin y: -15.2298 Å / Origin z: -8.6085 Å
111213212223313233
T-0.0514 Å20.0039 Å2-0.0041 Å2--0.0118 Å20.0125 Å2---0.0174 Å2
L0.0283 °20.142 °2-0.1162 °2-0.751 °2-0.3247 °2--2.1876 °2
S-0.0436 Å °-0.0091 Å °-0.0177 Å °0.0258 Å °0.0156 Å °-0.0517 Å °-0.0922 Å °0.0686 Å °0.0279 Å °

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