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- PDB-1p6p: Crystal Structure of Toad Liver Basic Fatty Acid-Binding Protein -

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Basic information

Entry
Database: PDB / ID: 1p6p
TitleCrystal Structure of Toad Liver Basic Fatty Acid-Binding Protein
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / BETA BARREL
Function / homology
Function and homology information


lipid transport / lipid binding / cytoplasm
Similarity search - Function
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
Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesBufo arenarum (Argentine toad)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDi Pietro, S.M. / Corsico, B. / Perduca, M. / Monaco, H.L. / Santome, J.A.
Citation
Journal: Biochemistry / Year: 2003
Title: Structural and Biochemical Characterization of Toad Liver Basic Fatty Acid-Binding Protein
Authors: Di Pietro, S.M. / Corsico, B. / Perduca, M. / Monaco, H.L. / Santome, J.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary X-ray Study of two Liver Basic Fatty Acid-Binding Proteins
Authors: Di Pietro, S.M. / Perduca, M. / Santome, J.A. / Monaco, H.L.
History
DepositionApr 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)13,9681
Polymers13,9681
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.140, 48.140, 135.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Fatty acid-binding protein, liver / L-FABP / Liver basic FABP / Lb- FABP


Mass: 13967.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bufo arenarum (Argentine toad) / Organ: Liver / References: UniProt: P83409
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Tris, PEG 1500, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, sitting drop
Details: Di Pietro, S.M., (2001) Acta Crystallogr.,Sect.D, 57, 1903.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
127-30 mg/mlprotein1drop
250 mMTris-HCl1droppH7.4
30.05 MTris-HCl1reservoirpH7.4
430 %(w/v)PEG15001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 2, 1999
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 5917 / Num. obs: 5917 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.064 / Net I/σ(I): 11.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 9 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 3 / Num. unique all: 832 / Rsym value: 0.252 / % possible all: 98.9
Reflection
*PLUS
Num. measured all: 47279 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 98.9 % / Rmerge(I) obs: 0.252

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
TNTrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: axolotl liver basic FABP model (unpublished)

Resolution: 2.5→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 565 -random
Rwork0.212 ---
all0.22 5827 --
obs0.22 5827 97.4 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 0 25 1005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.006
X-RAY DIFFRACTIONt_angle_deg1.413
X-RAY DIFFRACTIONt_dihedral_angle_d17.582
Refinement
*PLUS
Num. reflection all: 5827 / Num. reflection obs: 5266 / Num. reflection Rfree: 561
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.582
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.64 Å / Rfactor Rfree: 0.31 / Num. reflection Rfree: 54 / Rfactor Rwork: 0.269 / Num. reflection Rwork: 511

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