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- PDB-7fw5: Crystal Structure of human FABP4 with active site mutated to that... -

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Basic information

Entry
Database: PDB / ID: 7fw5
TitleCrystal Structure of human FABP4 with active site mutated to that of FABP3 in complex with palmitate
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
PALMITIC ACID / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / 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)15,3172
Polymers15,0601
Non-polymers2561
Water3,279182
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)35.757, 55.819, 74.734
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: 15060.242 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-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
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: Jan 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→44.72 Å / Num. obs: 53727 / % possible obs: 99.5 % / Redundancy: 6.428 % / Biso Wilson estimate: 18.615 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.053 / Χ2: 0.878 / Net I/σ(I): 15.09 / Num. measured all: 345384 / Scaling rejects: 472
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
1.15-1.186.250.884224361391738980.7820.96599.5
1.18-1.216.2540.8032.223897383538210.8290.87699.6
1.21-1.255.9310.8622.621898375336920.8480.94598.4
1.25-1.296.6630.53.5723939360035930.9370.54399.8
1.29-1.336.3820.5514.1722460354935190.9240.60199.2
1.33-1.376.6160.3085.6722561341534100.9680.33599.9
1.37-1.436.2760.2586.6320635329432880.9760.28299.8
1.43-1.486.8540.2149.1521632316131560.9840.23199.8
1.48-1.556.9040.14811.7921161307230650.9910.1699.8
1.55-1.636.8290.10515.7819886291629120.9950.11499.9
1.63-1.716.5280.08918.418115277727750.9950.09799.9
1.71-1.826.6450.06923.117569264626440.9970.07599.9
1.82-1.946.1920.06127.0815269249424660.9970.06798.9
1.94-2.16.680.0532.4715517233123230.9980.05499.7
2.1-2.35.7830.04833.0112174214721050.9970.05398
2.3-2.575.9530.04135.8111639196119550.9980.04599.7
2.57-2.976.780.03840.8911790174317390.9990.04199.8
2.97-3.646.4510.03442.279618149514910.9970.03799.7
3.64-5.145.7210.02940.346716118811740.9990.03298.8
5.14-44.726.4860.02642.6445477087010.9990.02999

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0093refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.15→44.72 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.672 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: FABP43 is mutated FABP4 with ligand binding site from FABP3
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 2460 5 %RANDOM
Rwork0.1797 ---
obs0.1814 47037 91.78 %-
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: 55.61 Å2 / Biso mean: 15.244 Å2 / Biso min: 10.85 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å20 Å20 Å2
2---0.89 Å20 Å2
3----1.3 Å2
Refinement stepCycle: final / Resolution: 1.15→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 36 182 1262
Biso mean--22.93 26.75 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221154
X-RAY DIFFRACTIONr_bond_other_d0.0010.02771
X-RAY DIFFRACTIONr_angle_refined_deg2.0721.9891555
X-RAY DIFFRACTIONr_angle_other_deg1.02431902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51324.58348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83215225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.731157
X-RAY DIFFRACTIONr_chiral_restr0.1060.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021248
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02221
X-RAY DIFFRACTIONr_rigid_bond_restr4.32536357
X-RAY DIFFRACTIONr_sphericity_free12.9895182
X-RAY DIFFRACTIONr_sphericity_bonded6.96151904
LS refinement shellResolution: 1.15→1.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 167 -
Rwork0.262 3236 -
all-3403 -
obs--91.09 %

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