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- PDB-7fxm: Crystal Structure of human FABP4 in complex with 5-cyclohexyl-2-h... -

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Basic information

Entry
Database: PDB / ID: 7fxm
TitleCrystal Structure of human FABP4 in complex with 5-cyclohexyl-2-hydroxybenzoic acid
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 / long-chain fatty acid binding / cellular response to lithium ion / Triglyceride catabolism / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / lipid droplet ...hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / Triglyceride catabolism / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / lipid droplet / cholesterol homeostasis / fatty acid binding / response to bacterium / positive regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / 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 protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
5-cyclohexyl-2-hydroxybenzoate / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Urban, R. / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,4344
Polymers15,0221
Non-polymers4113
Water3,153175
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)32.426, 53.773, 74.757
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-KWB / 5-cyclohexyl-2-hydroxybenzoate


Mass: 219.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.17 Å3/Da / Density % sol: 43.3 %
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: Oct 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.19→43.65 Å / Num. obs: 39966 / % possible obs: 93.4 % / Redundancy: 4.517 % / Biso Wilson estimate: 17.639 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.099 / Χ2: 0.84 / Net I/σ(I): 7.79 / Num. measured all: 180513 / Scaling rejects: 90
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
1.19-1.223.5880.8741.319306312525940.5381.00483
1.22-1.253.6570.7681.59614303826290.650.88386.5
1.25-1.293.5880.7221.619190293125610.7320.83387.4
1.29-1.333.8660.6212.0110005286125880.7520.71190.5
1.33-1.374.1250.5322.4310751282326060.8130.60492.3
1.37-1.424.1870.4782.8410619269225360.830.54294.2
1.42-1.484.2480.3793.5110543261824820.8910.42994.8
1.48-1.544.40.3134.410445251323740.9370.35494.5
1.54-1.64.8590.236.0111301240823260.9630.25796.6
1.6-1.685.0160.2037.2211175232622280.9710.22795.8
1.68-1.774.9640.1598.7510603218821360.9790.17897.6
1.77-1.884.6390.139.859417209820300.9880.14796.8
1.88-2.015.3140.09613.410303199119390.9930.10797.4
2.01-2.175.320.08215.439619184318080.9880.09298.1
2.17-2.385.2040.07416.938530169516390.9930.08396.7
2.38-2.664.5050.07116.546694155414860.9920.0895.6
2.66-3.075.3410.06519.617183138513450.9940.07297.1
3.07-3.765.7210.0722.416654119211630.9940.07797.6
3.76-5.325.5320.06822.6351619499330.9930.07598.3
5.32-43.656.0390.06823.5934005725630.9950.07498.4

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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: 1.19→43.65 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.7 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: bad data overall - maybe re-collect ligand placement and conformation safe
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 1880 5.1 %RANDOM
Rwork0.2086 ---
obs0.2104 35335 87.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 56.65 Å2 / Biso mean: 12.728 Å2 / Biso min: 7.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2---0.49 Å20 Å2
3----1.05 Å2
Refinement stepCycle: final / Resolution: 1.19→43.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 26 175 1241
Biso mean--22.79 21.73 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021126
X-RAY DIFFRACTIONr_bond_other_d0.0010.02775
X-RAY DIFFRACTIONr_angle_refined_deg2.0431.9781522
X-RAY DIFFRACTIONr_angle_other_deg1.15231904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.95224.34846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43915219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.313157
X-RAY DIFFRACTIONr_chiral_restr0.1190.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021227
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02224
X-RAY DIFFRACTIONr_rigid_bond_restr7.76831901
X-RAY DIFFRACTIONr_sphericity_free11.672541
X-RAY DIFFRACTIONr_sphericity_bonded5.54452021
LS refinement shellResolution: 1.19→1.221 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 114 -
Rwork0.349 1987 -
all-2101 -
obs--70.1 %

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