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- PDB-2q9s: Linoleic Acid Bound to Fatty Acid Binding Protein 4 -

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Basic information

Entry
Database: PDB / ID: 2q9s
TitleLinoleic Acid Bound to Fatty Acid Binding Protein 4
ComponentsFatty acid-binding protein
KeywordsLIPID BINDING PROTEIN / beta clamshell
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
LINOLEIC ACID / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGillilan, R.E. / Ayers, S.D. / Noy, N.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Basis for Activation of Fatty Acid-binding Protein 4.
Authors: Gillilan, R.E. / Ayers, S.D. / Noy, N.
History
DepositionJun 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3783
Polymers17,0021
Non-polymers3772
Water86548
1
A: Fatty acid-binding protein
hetero molecules

A: Fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7566
Polymers34,0032
Non-polymers7534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2360 Å2
ΔGint-33 kcal/mol
Surface area13150 Å2
MethodPISA
2
A: Fatty acid-binding protein
hetero molecules

A: Fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7566
Polymers34,0032
Non-polymers7534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
MethodPQS
Unit cell
Length a, b, c (Å)77.560, 96.267, 49.893
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-501-

SO4

DetailsThe assembly is a dimer. The second half is generated by [-x,y,1/2-z]

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Components

#1: Protein Fatty acid-binding protein / AFABP / Adipocyte lipid-binding protein / ALBP / A-FABP / P2 adipocyte protein / Myelin P2 protein ...AFABP / Adipocyte lipid-binding protein / ALBP / A-FABP / P2 adipocyte protein / Myelin P2 protein homolog / 3T3-L1 lipid-binding protein / 422 protein / P15 / FABP4


Mass: 17001.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fabp4 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04117
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EIC / LINOLEIC ACID / 9,12-LINOLEIC ACID


Mass: 280.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium Cacodylate, 0.1 M Ammonium Sulfate, 35% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9176 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 30, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9176 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 8446 / % possible obs: 98.7 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.082 / Χ2: 1.166 / Net I/σ(I): 24.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.176 / Num. unique all: 834 / Χ2: 1.158 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.1.24refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→12 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.819 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 402 4.8 %RANDOM
Rwork0.226 ---
obs0.228 8434 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.784 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 25 48 1085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221047
X-RAY DIFFRACTIONr_bond_other_d0.0020.02982
X-RAY DIFFRACTIONr_angle_refined_deg1.0141.9721400
X-RAY DIFFRACTIONr_angle_other_deg0.69532287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625130
X-RAY DIFFRACTIONr_chiral_restr0.0640.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02209
X-RAY DIFFRACTIONr_nbd_refined0.160.2150
X-RAY DIFFRACTIONr_nbd_other0.2190.21134
X-RAY DIFFRACTIONr_nbtor_other0.0780.2713
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.231
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0590.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0790.24
X-RAY DIFFRACTIONr_mcbond_it0.2631.5644
X-RAY DIFFRACTIONr_mcangle_it0.50921041
X-RAY DIFFRACTIONr_scbond_it0.8383403
X-RAY DIFFRACTIONr_scangle_it1.3824.5359
LS refinement shellResolution: 2.3→2.42 Å / Total num. of bins used: 10
RfactorNum. reflection
Rfree0.294 63
Rwork0.246 1110
obs-1173
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.94521.2213-5.47671.9147-0.189110.9831-0.03220.12590.3434-0.21810.0995-0.1673-1.83241.1709-0.06730.6933-0.39020.03010.3523-0.07590.255612.520422.1319-3.5522
23.29351.2786-0.79144.26441.98429.04810.1279-0.01140.1185-0.10670.0256-0.0898-1.39440.9189-0.15350.2223-0.1801-0.00340.15140.00410.12218.107712.841-3.3599
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 4025 - 64
2X-RAY DIFFRACTION2AA41 - 13165 - 155

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