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- PDB-1tw4: Crystal Structure of Chicken Liver Basic Fatty Acid Binding Prote... -

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Basic information

Entry
Database: PDB / ID: 1tw4
TitleCrystal Structure of Chicken Liver Basic Fatty Acid Binding Protein (Bile Acid Binding Protein) Complexed With Cholic Acid
ComponentsFatty acid-binding protein
KeywordsLIPID BINDING PROTEIN / Lb-FABP / FABP / BABP / INTRACELLULAR BILE ACID-BINDING PROTEIN / CHOLIC ACID / BILE ACID
Function / homology
Function and homology information


fatty acid transport / fatty acid binding / nucleus / 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 / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CHOLIC ACID / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNichesola, D. / Perduca, M. / Capaldi, S. / Carrizo, M.E. / Righetti, P.G. / Monaco, H.L.
Citation
Journal: Biochemistry / Year: 2004
Title: Crystal structure of chicken liver basic Fatty Acid-binding protein complexed with cholic acid
Authors: Nichesola, D. / Perduca, M. / Capaldi, S. / Carrizo, M.E. / Righetti, P.G. / Monaco, H.L.
#1: Journal: MOL.CELL.BIOCHEM. / Year: 1990
Title: Crystal Structure of Chicken Liver Basic Fatty Acid-Binding Protein at 2.7 A Resolution
Authors: Scapin, G. / Spadon, P. / Mammi, M. / Zanotti, G. / Monaco, H.L.
#2: Journal: FEBS Lett. / Year: 1988
Title: Chicken liver basic fatty acid-binding protein (pI = 9.0). Purification, crystallization and preliminary X-ray data
Authors: Scapin, G. / Spadon, P. / Pengo, L. / Mammi, M. / Zanotti, G. / Monaco, H.L.
History
DepositionJun 30, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Fatty acid-binding protein
B: Fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8356
Polymers28,2002
Non-polymers1,6344
Water4,486249
1
A: Fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9173
Polymers14,1001
Non-polymers8172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9173
Polymers14,1001
Non-polymers8172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.310, 63.410, 77.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fatty acid-binding protein / L-FABP / Liver basic FABP / LB- FABP / Bile Acid-Binding Protein


Mass: 14100.177 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: Liver / References: UniProt: P80226
#2: Chemical
ChemComp-CHD / CHOLIC ACID


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


Mass: 18.015 Da / Num. of mol.: 249 / 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: 53 %
Crystal growTemperature: 298 K / Method: microgravity / pH: 7.5
Details: IMIDAZOLE, PEG 6000, pH 7.5, MICROGRAVITY, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 12, 2001 / Details: Three-segment Pt-coated toroidal
RadiationMonochromator: Double Crystal (Si111, Si220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 19076 / Num. obs: 19076 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.552 Å2 / Rsym value: 0.063
Reflection shellResolution: 2.03→2.14 Å / Rsym value: 0.1 / % possible all: 80

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 8305654.73 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1864 9.8 %RANDOM
Rwork0.216 ---
all0.229 18927 --
obs0.216 18927 97.1 %-
Displacement parametersBiso mean: 24.27 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1978 0 116 249 2343
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.396
X-RAY DIFFRACTIONc_dihedral_angle_d26.357
X-RAY DIFFRACTIONc_improper_angle_d1.333
LS refinement shellResolution: 2→2.07 Å /
RfactorNum. reflection
Rfree0.271 39
Rwork0.229 -
obs-441

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