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- PDB-3em0: Crystal structure of Zebrafish Ileal Bile Acid-Bindin Protein com... -

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Basic information

Entry
Database: PDB / ID: 3em0
TitleCrystal structure of Zebrafish Ileal Bile Acid-Bindin Protein complexed with cholic acid (crystal form B).
ComponentsIleal Bile Acid-Binding Protein
KeywordsLIPID BINDING PROTEIN / Ileal bile acid-binding protein / zebrafish (Danio rerio) / 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 / 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
CHOLIC ACID / Gastrotropin
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

Downloads & links

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Assembly

Deposited unit
A: Ileal Bile Acid-Binding Protein
B: Ileal Bile Acid-Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,06011
Polymers30,3822
Non-polymers3,6779
Water1,24369
1
A: Ileal Bile Acid-Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8265
Polymers15,1911
Non-polymers1,6344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ileal Bile Acid-Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2346
Polymers15,1911
Non-polymers2,0435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.285, 85.285, 75.055
Angle α, β, γ (deg.)90.00, 127.65, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is the protein 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.: 2
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-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C24H40O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 4.02 Å3/Da / Density % sol: 69.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Sodium HEPES, 2.0 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.03 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2006 / Details: Double crystal (Si111, Si220)
RadiationMonochromator: Three-segment Pt-coated toroidal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 24125 / Num. obs: 24125 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 9.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 1.3 / Num. unique all: 2395 / Rsym value: 0.312 / % possible all: 97.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELZ

3elz


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.728 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.215 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25422 1237 5.1 %RANDOM
Rwork0.22566 ---
all0.2272 24125 --
obs0.2272 22888 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.977 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20.34 Å2
2--0.53 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 261 69 2385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222382
X-RAY DIFFRACTIONr_angle_refined_deg1.5362.0583282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4765264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.92325.63287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10615378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.375155
X-RAY DIFFRACTIONr_chiral_restr0.0960.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021583
X-RAY DIFFRACTIONr_nbd_refined0.2020.2903
X-RAY DIFFRACTIONr_nbtor_refined0.330.21630
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2117
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.22
X-RAY DIFFRACTIONr_mcbond_it0.5891.51350
X-RAY DIFFRACTIONr_mcangle_it1.00322116
X-RAY DIFFRACTIONr_scbond_it1.41431143
X-RAY DIFFRACTIONr_scangle_it2.164.51166
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 87 -
Rwork0.272 1622 -
obs-1709 96.28 %
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)
12.01310.12170.59461.3101-1.09412.3957-0.0153-0.11560.15970.134-0.0468-0.0001-0.20640.05230.0621-0.0476-0.04310.0003-0.0665-0.0761-0.0228-16.66984.4186-18.8578
23.45351.6103-1.04651.636-0.79982.023-0.13180.1125-0.0202-0.04650.1347-0.00820.06280.0299-0.0029-0.0822-0.02840.0229-0.06960.0165-0.0646-39.7087-17.3581-11.3649
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 129
2X-RAY DIFFRACTION1A150
3X-RAY DIFFRACTION1A151
4X-RAY DIFFRACTION1A152
5X-RAY DIFFRACTION1A153
6X-RAY DIFFRACTION2B0 - 129
7X-RAY DIFFRACTION2B150
8X-RAY DIFFRACTION2B151
9X-RAY DIFFRACTION2B152
10X-RAY DIFFRACTION2B153
11X-RAY DIFFRACTION2B500

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