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- PDB-7fzr: Crystal Structure of human FABP4 in complex with 4-hydroxy-6-(2-n... -

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Basic information

Entry
Database: PDB / ID: 7fzr
TitleCrystal Structure of human FABP4 in complex with 4-hydroxy-6-(2-naphthalen-1-ylethyl)pyran-2-one
ComponentsFatty acid-binding protein, adipocyte
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING
Function / homology
Function and homology information


hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / lipid droplet ...hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / lipid droplet / cholesterol homeostasis / fatty acid binding / response to bacterium / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin
Similarity search - Domain/homology
FORMIC ACID / Chem-WHN / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Maurer, M. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To be published
Title: Crystal Structure of a human FABP4 complex
Authors: Obst, U. / Magnone, C. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein, adipocyte
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5275
Polymers15,0221
Non-polymers5044
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.396, 53.936, 75.085
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fatty acid-binding protein, adipocyte / Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / A-FABP / AFABP ...Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / A-FABP / AFABP / Fatty acid-binding protein 4


Mass: 15022.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15090
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-WHN / 4-hydroxy-6-[2-(naphthalen-1-yl)ethyl]-2H-pyran-2-one


Mass: 266.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.12→43.81 Å / Num. obs: 50543 / % possible obs: 98.7 % / Redundancy: 6.02 % / Biso Wilson estimate: 13.967 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.037 / Rsym value: 0.036 / Χ2: 0.958 / Net I/σ(I): 24.19 / Num. measured all: 305197
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.12-1.154.6260.1838.115118372832680.9710.20687.7
1.15-1.185.9010.15910.9620932360935470.9860.17598.3
1.18-1.225.8590.14411.9420448354234900.9880.15998.5
1.22-1.255.7710.12713.119839348034380.9920.1498.8
1.25-1.36.2710.09915.9820726332133050.9950.10999.5
1.3-1.346.2160.08817.8920128324732380.9950.09799.7
1.34-1.396.0760.07819.9518689307830760.9960.08699.9
1.39-1.455.9730.06722.7917991302030120.9960.07399.7
1.45-1.516.450.05527.2118678289828960.9980.0699.9
1.51-1.596.4490.04731.9817748275727520.9980.05199.8
1.59-1.676.3040.04235.1716648264426410.9980.04699.9
1.67-1.775.8870.03937.3114807251825150.9980.04299.9
1.77-1.96.6070.03344.0215651237023690.9990.036100
1.9-2.056.460.03147.8214244220722050.9990.03499.9
2.05-2.246.2550.03249.0712653202720230.9990.03599.8
2.24-2.515.6820.03148.0810609187618670.9990.03499.5
2.51-2.96.5970.02853.5810826164316410.9990.03199.9
2.9-3.556.3520.02854.029026142714210.9990.0399.6
3.55-5.025.6320.02651.946268111511130.9990.02999.8
5.02-43.816.1660.02653.541686806760.9980.02899.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0119refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.12→43.81 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.679 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: head group has two conformations, one planar, the other bent
RfactorNum. reflection% reflectionSelection details
Rfree0.1481 2543 5.1 %RANDOM
Rwork0.121 ---
obs0.1224 47525 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.05 Å2 / Biso mean: 13.225 Å2 / Biso min: 5.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 1.12→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 82 244 1372
Biso mean--14.39 24.74 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021188
X-RAY DIFFRACTIONr_bond_other_d0.0010.021172
X-RAY DIFFRACTIONr_angle_refined_deg2.2022.0021616
X-RAY DIFFRACTIONr_angle_other_deg0.8763.0012672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3115156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93325.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71315229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.223156
X-RAY DIFFRACTIONr_chiral_restr0.1270.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021306
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02255
X-RAY DIFFRACTIONr_rigid_bond_restr5.51632360
X-RAY DIFFRACTIONr_sphericity_free21.83563
X-RAY DIFFRACTIONr_sphericity_bonded9.65852512
LS refinement shellResolution: 1.122→1.151 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.179 147 -
Rwork0.153 2868 -
all-3015 -
obs--84.62 %

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