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- PDB-3js1: Crystal structure of adipocyte fatty acid binding protein covalen... -

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Basic information

Entry
Database: PDB / ID: 3js1
TitleCrystal structure of adipocyte fatty acid binding protein covalently modified with 4-hydroxy-2-nonenal
ComponentsAdipocyte fatty acid-binding protein
KeywordsLIPID BINDING PROTEIN / fatty acid binding protein / 4-hydroxy-2-nonenal modified cysteine
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 / cytoplasm / cytosol
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
PHOSPHATE ION / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.81 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 9, 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_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 fatty acid-binding protein
B: Adipocyte fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4873
Polymers29,3922
Non-polymers951
Water6,575365
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.331, 81.310, 92.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAuthors state that the biological assembly is a dimer, equal to the contents in the asymmetric unit.

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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: 14695.911 Da / Num. of mol.: 2
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-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.: 365 / 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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.9 M Sodium/potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 20, 2008 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 35084 / Num. obs: 35084 / % possible obs: 97.4 % / Redundancy: 4.4 % / Rsym value: 0.068 / Net I/σ(I): 20.28
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.49 / Num. unique all: 1107 / Rsym value: 0.717 / % possible all: 63.6

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Processing

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

1lie


Resolution: 1.81→19.86 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22771 1752 5 %RANDOM
Rwork0.19674 ---
obs0.19827 33276 99.16 %-
all-33276 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.863 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.81→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 5 365 2426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222086
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9732794
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1385258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.68224.35385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.815399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2011514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021474
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2490.2949
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21422
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8391.51289
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49722084
X-RAY DIFFRACTIONr_scbond_it2.5723797
X-RAY DIFFRACTIONr_scangle_it4.2084.5709
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.86 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 128 -
Rwork0.328 2422 -
obs-2550 99.69 %

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