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- PDB-1lie: X-RAY CRYSTALLOGRAPHIC STRUCTURES OF ADIPOCYTE LIPID BINDING PROT... -

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Basic information

Entry
Database: PDB / ID: 1lie
TitleX-RAY CRYSTALLOGRAPHIC STRUCTURES OF ADIPOCYTE LIPID BINDING PROTEIN COMPLEXED WITH PALMITATE AND HEXADECANESULFONIC ACID. PROPERTIES OF CAVITY BINDING SITES
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
PALMITIC ACID / PROPANOIC ACID / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsLalonde, J.M. / Bernlohr, D.A. / Banaszak, L.J.
CitationJournal: Biochemistry / Year: 1994
Title: X-ray crystallographic structures of adipocyte lipid-binding protein complexed with palmitate and hexadecanesulfonic acid. Properties of cavity binding sites.
Authors: LaLonde, J.M. / 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 1.4Mar 26, 2025Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: ADIPOCYTE LIPID-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9183
Polymers14,5881
Non-polymers3312
Water1,47782
1
A: ADIPOCYTE LIPID-BINDING PROTEIN
hetero molecules

A: ADIPOCYTE LIPID-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8366
Polymers29,1752
Non-polymers6614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Unit cell
Length a, b, c (Å)119.540, 37.860, 28.570
Angle α, β, γ (deg.)90.00, 92.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ADIPOCYTE LIPID-BINDING PROTEIN


Mass: 14587.687 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P04117
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal grow
*PLUS
Method: batch method / PH range low: 7.2 / PH range high: 6.6
Components of the solutions
*PLUS
Conc.: 2.1-3.0 M / Chemical formula: NaH2PO4-K2HPO4

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 16514 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Num. measured all: 73035 / Rmerge(I) obs: 0.0363

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.6→10 Å
RfactorNum. reflection
Rfree0.239 -
Rwork0.198 -
obs0.198 15995
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 23 82 1128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
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_deg1.65
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: 0.198 / Rfactor Rfree: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.9 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.65

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