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- PDB-1lif: THE ADIPOCYTE LIPID-BINDING PROTEIN AT 1.6 ANGSTROMS RESOLUTION: ... -

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Basic information

Entry
Database: PDB / ID: 1lif
TitleTHE ADIPOCYTE LIPID-BINDING PROTEIN AT 1.6 ANGSTROMS RESOLUTION: CRYSTAL STRUCTURES OF THE APOPROTEIN AND WITH BOUND SATURATED AND UNSATURATED FATTY ACIDS
ComponentsADIPOCYTE LIPID-BINDING PROTEIN
KeywordsLIPID BINDING PROTEIN / LIPID-BINDING PROTEIN
Function / homology
Function and homology information


Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / cholesterol homeostasis / response to bacterium ...Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / cholesterol homeostasis / response to bacterium / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
STEARIC ACID / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsZu, Z. / Bernlohr, D.A. / Banaszak, L.J.
Citation
Journal: J.Biol.Chem. / Year: 1993
Title: The adipocyte lipid-binding protein at 1.6-A resolution. Crystal structures of the apoprotein and with bound saturated and unsaturated fatty acids.
Authors: Xu, Z. / Bernlohr, D.A. / Banaszak, L.J.
#1: Journal: Biochemistry / Year: 1992
Title: Crystal Structure of Recombinant Murine Adipocyte Lipid-Binding Protein
Authors: Xu, Z. / Bernlohr, D.A. / Banaszak, L.J.
History
DepositionDec 21, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Structure summary
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type / struct_keywords
Item: _pdbx_database_status.process_site / _struct_keywords.text
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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: ADIPOCYTE LIPID-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8242
Polymers14,5401
Non-polymers2841
Water1,74797
1
A: ADIPOCYTE LIPID-BINDING PROTEIN
hetero molecules

A: ADIPOCYTE LIPID-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6484
Polymers29,0792
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Unit cell
Length a, b, c (Å)120.530, 37.860, 28.730
Angle α, β, γ (deg.)90.00, 92.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ADIPOCYTE LIPID-BINDING PROTEIN


Mass: 14539.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P04117
#2: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 6.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
21.25 Msodium1drop
32.5 Msodium1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.48 Å / Num. obs: 19986 / % possible obs: 65.1 % / Num. measured all: 65555 / Rmerge(I) obs: 0.0286

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.18 / Rfactor obs: 0.18 / Highest resolution: 1.6 Å
Details: LYS 9, LYS 21, MET 35, LYS 37, LYS 79, AND LYS 120 POSITIONS ARE NOT ACCURATE.
Refinement stepCycle: LAST / Highest resolution: 1.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 20 97 1134
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.8

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