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- PDB-1lfo: LIVER FATTY ACID BINDING PROTEIN-OLEATE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1lfo
TitleLIVER FATTY ACID BINDING PROTEIN-OLEATE COMPLEX
ComponentsLIVER FATTY ACID BINDING PROTEIN
KeywordsINTRACELLULAR LIPID TRANSPORT PROTEIN / FATTY ACID BINDING PROTEIN
Function / homology
Function and homology information


acylglycerol metabolic process / digestive system process / hepatic stellate cell activation / monoacylglycerol metabolic process / acylglycerol biosynthetic process / fatty acid primary amide metabolic process / fatty acid derivative metabolic process / endocannabinoid signaling pathway / diterpenoid metabolic process / Regulation of lipid metabolism by PPARalpha ...acylglycerol metabolic process / digestive system process / hepatic stellate cell activation / monoacylglycerol metabolic process / acylglycerol biosynthetic process / fatty acid primary amide metabolic process / fatty acid derivative metabolic process / endocannabinoid signaling pathway / diterpenoid metabolic process / Regulation of lipid metabolism by PPARalpha / chylomicron assembly / long-chain fatty acyl-CoA binding / Triglyceride catabolism / : / lysophospholipid:sodium symporter activity / ketone body metabolic process / long-chain fatty acid import into cell / connective tissue replacement / Heme degradation / reduction of food intake in response to dietary excess / Cytoprotection by HMOX1 / cannabinoid signaling pathway / intracellular signaling cassette / long-chain fatty acid metabolic process / lipid droplet formation / ketone metabolic process / response to tetrachloromethane / sterol binding / oleic acid binding / unsaturated fatty acid biosynthetic process / bile acid secretion / glycerol metabolic process / aldehyde metabolic process / adult feeding behavior / D-glucose transmembrane transport / arachidonate metabolic process / apical cortex / lipoprotein transport / triglyceride biosynthetic process / positive regulation of fatty acid beta-oxidation / smooth muscle tissue development / very-low-density lipoprotein particle clearance / response to fatty acid / lipoprotein metabolic process / vesicle budding from membrane / L-glutamine metabolic process / bile acid metabolic process / bile acid binding / response to cholesterol / response to vitamin B3 / digestive tract development / retinol metabolic process / cellular detoxification / heterocyclic compound binding / intestinal absorption / cholesterol efflux / long-chain fatty acid transmembrane transporter activity / triglyceride homeostasis / triglyceride metabolic process / response to food / cholesterol binding / response to starvation / response to lipid / fatty acid beta-oxidation / fatty acid oxidation / antioxidant activity / peroxisomal matrix / long-chain fatty acid transport / xenobiotic transport / fatty acid transport / cholesterol metabolic process / energy homeostasis / phospholipid metabolic process / response to nutrient / cholesterol homeostasis / fatty acid binding / establishment of localization in cell / glycolytic process / glutathione metabolic process / lipid metabolic process / liver development / fatty acid metabolic process / phospholipid binding / multicellular organism growth / glucose metabolic process / cellular response to hydrogen peroxide / fatty acid biosynthetic process / response to oxidative stress / cellular response to hypoxia / gene expression / cell population proliferation / response to xenobiotic stimulus / inflammatory response / chromatin binding / lipid binding / protein-containing complex / nucleoplasm / membrane / nucleus / 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
BUTENOIC ACID / OLEIC ACID / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsThompson, J. / Winter, N. / Terwey, D. / Bratt, J. / Banaszak, L.
CitationJournal: J.Biol.Chem. / Year: 1997
Title: The crystal structure of the liver fatty acid-binding protein. A complex with two bound oleates.
Authors: Thompson, J. / Winter, N. / Terwey, D. / Bratt, J. / Banaszak, L.
History
DepositionDec 9, 1996Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIVER FATTY ACID BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9855
Polymers14,3341
Non-polymers6514
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.890, 83.890, 44.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein LIVER FATTY ACID BINDING PROTEIN / LFABP


Mass: 14333.608 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: AMINO-TERMINAL INITIATOR METHIONINE AND MODIFIED CYSTEINE 69 PRESENT
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Plasmid: PJBL2 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 H1 / References: UniProt: P02692
#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-BEO / BUTENOIC ACID


Mass: 86.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O2
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 55 %
Description: DATA IN THE 2.3 - 2.1 ANGSTROM RANGE WAS NOT USED DUE TO ITS POOR QUALITY.
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: HANGING DROP VAPOR DIFFUSION EXPERIMENT 1 ML WELL: 3 M AMMONIUM SULFATE, 200 MM LISO4, 100 MM CITRATE, AT A PH OF 5.6 STOCK: 13 MG/ML LFABP-OLEATE COMPLEX 10 MICROLITER DROP: 1:1 MIXTURE OF ...Details: HANGING DROP VAPOR DIFFUSION EXPERIMENT 1 ML WELL: 3 M AMMONIUM SULFATE, 200 MM LISO4, 100 MM CITRATE, AT A PH OF 5.6 STOCK: 13 MG/ML LFABP-OLEATE COMPLEX 10 MICROLITER DROP: 1:1 MIXTURE OF STOCK AND WELL, vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 Mammonium sulfate1reservoir
2200 mM1reservoirLiSO4
3100 mMcitrate1reservoir
41.5 Mammonium sulfate1drop
5100 mM1dropLiSO4
650 mMcitrate1drop
76.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 26, 1991
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→38.8 Å / Num. obs: 8640 / % possible obs: 79.3 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 36.8 Å2 / Rsym value: 0.1 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.3 Å / Mean I/σ(I) obs: 0.89 / Rsym value: 0.535 / % possible all: 33.2
Reflection
*PLUS
Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 33.2 % / Num. unique obs: 940 / Rmerge(I) obs: 0.535

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SUPERIMPOSED POLYALANINE COMPOSITE STRUCTURE OF 1ADL, 1CBR, 1CRB, 1OPB, 1IFC, 1HMR

1adl

1cbr

1crb

1opb

1ifc

1hmr


Resolution: 2.3→8 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.262 396 5.3 %RANDOM
Rwork0.202 ---
obs0.202 7475 92.6 %-
Displacement parametersBiso mean: 40.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å-
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1004 0 46 62 1112
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.53
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.11
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.381.5
X-RAY DIFFRACTIONx_mcangle_it2.042
X-RAY DIFFRACTIONx_scbond_it2.182
X-RAY DIFFRACTIONx_scangle_it2.72.5
LS refinement shellResolution: 2.3→2.33 Å / Rfactor Rfree error: 0.131 / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.45 12 3 %
Rwork0.46 153 -
obs--61.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2OLEATE.PAROLEATE.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.11

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