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- PDB-1g7n: Toward changing specificity: adipocyte lipid binding protein muta... -

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Basic information

Entry
Database: PDB / ID: 1g7n
TitleToward changing specificity: adipocyte lipid binding protein mutant, apo form
ComponentsADIPOCYTE LIPID-BINDING PROTEIN
KeywordsLIPID BINDING PROTEIN / fatty acid binding protein / beta barrel / protein engineering
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
PHOSPHATE ION / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 1.5 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 10, 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 / 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)14,6212
Polymers14,5261
Non-polymers951
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.080, 37.970, 28.820
Angle α, β, γ (deg.)90.00, 92.32, 90.00
Int Tables number5
Space group name H-MC121

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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: PRSET / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium/potassium phosphate, pH 7.0, 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: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 2, 1998
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→36 Å / Num. all: 20871 / Num. obs: 17873 / % possible obs: 85.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.87 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 34.5
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 0.54 % / Rmerge(I) obs: 0.2292 / Num. unique all: 1857 / % possible all: 37.6
Reflection
*PLUS
Lowest resolution: 8 Å / Num. obs: 31800 / % possible obs: 89 % / Redundancy: 2.61 % / Num. measured all: 83041 / Rmerge(I) obs: 0.045

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
X-PLORmodel building
CNSrefinement
X-PLORphasing
RefinementStarting model: PDB 1LIB without waters, ligand, alternative conformations, or ions

1lib


Resolution: 1.5→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: X-PLOR was also used for refinement. The following amino acids have alternative conformations: Cys1, Asp2, Val11, Glu14, Met20, Glu22, Val32, Ser53, Glu73, Ile83, Thr103, Leu113, Glu129, and Ala131.
RfactorNum. reflectionSelection details
Rfree0.2253 1718 random
Rwork0.1964 --
all-20798 -
obs-17717 -
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 5 84 1212
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d0.63
LS refinement shellResolution: 1.5022→1.559 Å /
Num. reflection% reflection
obs1299 37.6 %
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor Rfree: 0.225 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.63

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