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

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Basic information

Entry
Database: PDB / ID: 3elz
TitleCrystal structure of Zebrafish Ileal Bile Acid-Bindin Protein complexed with cholic acid (crystal form A).
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
C: ileal Bile Acid-Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,88516
Polymers45,5743
Non-polymers5,31113
Water1,26170
1
A: 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
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
3
C: ileal Bile Acid-Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4174
Polymers15,1911
Non-polymers1,2263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.195, 80.290, 39.723
Angle α, β, γ (deg.)90.00, 96.12, 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.: 3
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.: 13 / Source method: obtained synthetically / Formula: C24H40O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1 M tri-sodium citrate dihydrate., pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2006 / Details: Toroidal mirror
RadiationMonochromator: Si 311 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 22845 / Num. obs: 22845 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 16.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2885 / Rsym value: 0.347 / % possible all: 84.4

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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: 3ELX

3elx


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / SU B: 15.666 / SU ML: 0.204 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.345 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26426 1164 5.1 %RANDOM
Rwork0.22181 ---
all0.22404 22837 --
obs0.22404 21673 96.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.916 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å2-0.33 Å2
2--0.02 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3090 0 377 70 3537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223566
X-RAY DIFFRACTIONr_angle_refined_deg1.4622.0564909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7065398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89425.692130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.14715569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.47157
X-RAY DIFFRACTIONr_chiral_restr0.0910.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022384
X-RAY DIFFRACTIONr_nbd_refined0.2010.21367
X-RAY DIFFRACTIONr_nbtor_refined0.3280.22450
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2138
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.24
X-RAY DIFFRACTIONr_mcbond_it0.3571.52040
X-RAY DIFFRACTIONr_mcangle_it0.6523186
X-RAY DIFFRACTIONr_scbond_it0.92131701
X-RAY DIFFRACTIONr_scangle_it1.3664.51723
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 67 -
Rwork0.27 1316 -
obs-1383 80.31 %
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)
14.3157-0.11290.82911.50240.54154.4344-0.0587-0.21650.0386-0.04470.01230.2196-0.005-0.34220.0464-0.2393-0.0369-0.0628-0.14290.0573-0.1301-9.50323.3294-10.1132
24.220.3534-0.8893.0373-0.18253.949-0.03150.2007-0.2322-0.1196-0.11130.0270.275-0.24830.1428-0.1229-0.0657-0.0255-0.1742-0.0496-0.1504-40.8975-4.7257-22.8807
32.5929-0.85-0.74176.18571.66377.33740.37750.04290.3257-0.1275-0.12210.1173-1.0153-0.7871-0.25540.13550.10020.1745-0.09210.00660.0089-51.706914.5194-6.485
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 130
2X-RAY DIFFRACTION1A150
3X-RAY DIFFRACTION1A151
4X-RAY DIFFRACTION1A152
5X-RAY DIFFRACTION1A153
6X-RAY DIFFRACTION1A200
7X-RAY DIFFRACTION2B-2 - 131
8X-RAY DIFFRACTION2B150
9X-RAY DIFFRACTION2B151
10X-RAY DIFFRACTION2B152
11X-RAY DIFFRACTION2B153
12X-RAY DIFFRACTION2B200
13X-RAY DIFFRACTION3C0 - 133
14X-RAY DIFFRACTION3C150
15X-RAY DIFFRACTION3C151
16X-RAY DIFFRACTION3C153

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