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- PDB-1g74: Toward changing specificity: adipocyte lipid binding protein muta... -

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Basic information

Entry
Database: PDB / ID: 1g74
TitleToward changing specificity: adipocyte lipid binding protein mutant, oleic acid bound form
ComponentsADIPOCYTE LIPID-BINDING PROTEIN
KeywordsLIPID BINDING PROTEIN / beta-barrel / fatty acid binding protein / protein engineering / fatty acid binding
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
OLEIC ACID / PHOSPHATE ION / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / isomorphous with apo EF-ALBP (PDB 1G7N) / Resolution: 1.7 Å
AuthorsReese, A.J. / Banaszak, L.J.
CitationJournal: J.Lipid Res. / Year: 2004
Title: Specificity determinants for lipids bound to beta-barrel proteins.
Authors: Reese, A.J. / Banaszak, L.J.
History
DepositionNov 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)14,9033
Polymers14,5261
Non-polymers3772
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.920, 36.890, 27.870
Angle α, β, γ (deg.)90.00, 92.61, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-21-

LYS

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Components

#1: Protein ADIPOCYTE LIPID-BINDING PROTEIN


Mass: 14525.663 Da / Num. of mol.: 1 / Mutation: I73E,A75V,D77G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ALBP / Plasmid: RSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04117
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-OLA / OLEIC ACID


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


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.1 Å3/Da / Density % sol: 41.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: sodium/potassium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19.0 mg/mlprotein1drop
212.5 MHEPES1droppH7.2
31.5-3 Msodium potassium phosphate1reservoir
424-34 %PEG40001reservoir
50.1-0.2 M1reservoirpH7.4NaAc
60.1 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 13, 2000 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.71→27 Å / Num. obs: 12433 / % possible obs: 93.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.31 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 16.4
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 3.37 % / Rmerge(I) obs: 0.304 / % possible all: 90.1
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 25 Å / Num. obs: 13235 / Redundancy: 3.19 % / Num. measured all: 42285

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Processing

Software
NameClassification
CNSrefinement
CNSphasing
RefinementMethod to determine structure: isomorphous with apo EF-ALBP (PDB 1G7N)
Starting model: EF-ALBP (PDB 1G7N)

1g7n


Resolution: 1.7→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The following amino acids have alternative conformations: Cys1, Lys9, Lys21, Glu22, Val44, Thr74, Glu116, Ser124, Glu129, and Oleate132
RfactorNum. reflectionSelection details
Rfree0.2378 604 random
Rwork0.2084 --
all-13476 -
obs-12432 -
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 45 119 1251
LS refinement shellResolution: 1.71→1.77 Å /
Num. reflection% reflection
obs1189 90 %
Refinement
*PLUS
Rfactor Rfree: 0.237 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.008
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.4

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