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- PDB-2ftb: Crystal structure of axolotl (Ambystoma mexicanum) liver bile aci... -

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Basic information

Entry
Database: PDB / ID: 2ftb
TitleCrystal structure of axolotl (Ambystoma mexicanum) liver bile acid-binding protein bound to oleic acid
ComponentsFatty acid-binding protein 2, liver
KeywordsLIPID BINDING PROTEIN / liver bile acid-binding protein / liver basic fatty acid-binding protein / axolotl / oleic acid / BABP / Lb-FABP
Function / homology
Function and homology information


lipid binding / cytoplasm
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 / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
OLEIC ACID / Fatty acid-binding protein 2, liver
Similarity search - Component
Biological speciesAmbystoma mexicanum (axolotl)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCapaldi, S. / Guariento, M. / Perduca, M. / Di Pietro, S.M. / Santome, J.A. / Monaco, H.L.
Citation
Journal: Proteins / Year: 2006
Title: Crystal structure of axolotl (Ambystoma mexicanum) liver bile acid-binding protein bound to cholic and oleic acid
Authors: Capaldi, S. / Guariento, M. / Perduca, M. / Di Pietro, S.M. / Santome, J.A. / Monaco, H.L.
#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
DepositionJan 24, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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: Fatty acid-binding protein 2, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0412
Polymers13,7591
Non-polymers2821
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.434, 66.434, 61.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-151-

HOH

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Components

#1: Protein Fatty acid-binding protein 2, liver / Bile acid-binding protein / L-FABP / Liver basic FABP / LB- FABP


Mass: 13758.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ambystoma mexicanum (axolotl) / Tissue: liver / References: UniProt: P81400
#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 0.2M sodium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 9, 2000 / Details: graphite crystal monochromator
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→45 Å / Num. all: 9823 / Num. obs: 9823 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.041
Reflection shellResolution: 2→2.05 Å / Rsym value: 0.185 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TVQ

1tvq


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.95 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26197 469 4.8 %RANDOM
Rwork0.21544 ---
all0.21755 9318 --
obs0.21755 9318 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.801 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 20 37 1023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022998
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9651341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9815124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.5726.04743
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91215181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.614154
X-RAY DIFFRACTIONr_chiral_restr0.0680.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02723
X-RAY DIFFRACTIONr_nbd_refined0.1740.2291
X-RAY DIFFRACTIONr_nbtor_refined0.2940.2632
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.210
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.22
X-RAY DIFFRACTIONr_mcbond_it0.7471.5647
X-RAY DIFFRACTIONr_mcangle_it1.26721007
X-RAY DIFFRACTIONr_scbond_it1.5263399
X-RAY DIFFRACTIONr_scangle_it2.4654.5334
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 31 -
Rwork0.239 666 -
obs--100 %

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