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- PDB-3jsq: Crystal structure of adipocyte fatty acid binding protein non-cov... -

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Basic information

Entry
Database: PDB / ID: 3jsq
TitleCrystal structure of adipocyte fatty acid binding protein non-covalently modified with 4-hydroxy-2-nonenal
ComponentsAdipocyte fatty acid-binding protein
KeywordsLIPID BINDING PROTEIN / fatty acid binding protein
Function / homology
Function and homology information


Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / fatty acid metabolic process ...Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / fatty acid metabolic process / cholesterol homeostasis / fatty acid binding / 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 / positive regulation of cell population proliferation / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(2E,4R)-4-HYDROXYNON-2-ENAL / PHOSPHATE ION / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHellberg, K. / Grimsrud, P.A. / Kruse, A.C. / Banaszak, L.J. / Ohlendorf, D.H. / Bernlohr, D.A.
CitationJournal: Protein Sci. / Year: 2010
Title: X-ray crystallographic analysis of adipocyte fatty acid binding protein (aP2) modified with 4-hydroxy-2-nonenal.
Authors: Hellberg, K. / Grimsrud, P.A. / Kruse, A.C. / Banaszak, L.J. / Ohlendorf, D.H. / Bernlohr, D.A.
History
DepositionSep 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Adipocyte fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1117
Polymers14,5401
Non-polymers5726
Water1,63991
1
A: Adipocyte fatty acid-binding protein
hetero molecules

A: Adipocyte fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,22214
Polymers29,0792
Non-polymers1,14312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)77.583, 93.174, 49.137
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-200-

CL

DetailsAuthors state that the assembly is a dimer. The second part of the biological assembly is generated by the two fold axis: [-X,Y,1/2-Z] as shown in remark 350

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Components

#1: Protein Adipocyte fatty acid-binding protein / A-FABP / AFABP / Fatty acid-binding protein 4 / Adipocyte lipid-binding protein / ALBP / P2 ...A-FABP / AFABP / Fatty acid-binding protein 4 / Adipocyte lipid-binding protein / ALBP / P2 adipocyte protein / Myelin P2 protein homolog / 3T3-L1 lipid-binding protein / Protein 422 / P15


Mass: 14539.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fabp4, Ap2 / Plasmid: Modified pRSETb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P04117
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-HNE / (2E,4R)-4-HYDROXYNON-2-ENAL


Mass: 156.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 1.6 M Sodium/potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 29, 2008 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 7758 / Num. obs: 7758 / % possible obs: 93.7 % / Redundancy: 3.6 % / Rsym value: 0.065 / Net I/σ(I): 16.63
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.85 / Num. unique all: 297 / Rsym value: 0.332 / % possible all: 73.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREP9.4.09phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LIE

1lie


Resolution: 2.3→19.97 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.325 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.263 364 4.7 %RANDOM
Rwork0.214 ---
obs0.216 7381 93.98 %-
all-7381 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.42 Å2 / Biso mean: 34.676 Å2 / Biso min: 16.97 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 32 91 1140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221061
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9821426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.4985132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19624.41943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65215201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.395157
X-RAY DIFFRACTIONr_chiral_restr0.0820.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02754
X-RAY DIFFRACTIONr_nbd_refined0.2280.2440
X-RAY DIFFRACTIONr_nbtor_refined0.3160.2713
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.294
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.26
X-RAY DIFFRACTIONr_mcbond_it1.0241.5648
X-RAY DIFFRACTIONr_mcangle_it1.99121051
X-RAY DIFFRACTIONr_scbond_it2.8463413
X-RAY DIFFRACTIONr_scangle_it4.8024.5374
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 24 -
Rwork0.253 443 -
all-467 -
obs-467 77.7 %

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