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- PDB-7fvz: Crystal Structure of human FABP4 in complex with (E)-6-(5-methoxy... -

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Basic information

Entry
Database: PDB / ID: 7fvz
TitleCrystal Structure of human FABP4 in complex with (E)-6-(5-methoxy-3,6,7-trimethyl-1,2-benzoxazol-4-yl)-4-methyl-hex-4-enoic 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 / 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 protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
FORMIC ACID / Chem-IZ7 / 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. / 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 binding site mutated to that of FABP5 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)15,5785
Polymers15,0221
Non-polymers5564
Water2,972165
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)32.445, 53.811, 75.017
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 / Mutation: V24L,V33M,A34G,M41C,S54T,F58L,H94Q,S125C
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-IZ7 / (4E)-6-(5-methoxy-3,6,7-trimethyl-1,2-benzoxazol-4-yl)-4-methylhex-4-enoic acid


Mass: 317.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 43.57 %
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 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.12→37.51 Å / Num. obs: 50131 / % possible obs: 98.2 % / Redundancy: 6.12 % / Biso Wilson estimate: 13.938 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.027 / Rrim(I) all: 0.028 / Rsym value: 0.027 / Χ2: 0.975 / Net I/σ(I): 31.38 / Num. measured all: 310052
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
1.12-1.154.8920.11810.4915428371131540.9880.13285
1.15-1.186.1470.10813.5521288360534630.9930.11896.1
1.18-1.226.0290.09814.5120651353734250.9940.10896.8
1.22-1.255.9430.0915.9320255346534080.9950.09998.4
1.25-1.36.4260.07918.4621066332132780.9960.08698.7
1.3-1.346.3650.07121.0120317321631920.9970.07799.3
1.34-1.396.2170.06323.2619248310730960.9970.06899.6
1.39-1.456.1050.05426.6718326301130020.9980.05999.7
1.45-1.516.5890.04930.7418885287328660.9980.05399.8
1.51-1.596.5680.0436.5618063275727500.9990.04399.7
1.59-1.676.4390.03641.2616921264426280.9990.03999.4
1.67-1.776.0480.03245.3115024249124840.9990.03599.7
1.77-1.96.7540.02854.2516006237523700.9990.0399.8
1.9-2.056.5970.02460.814519220522010.9990.02699.8
2.05-2.246.3850.02265.1312904202520210.9990.02499.8
2.24-2.515.7950.02264.1310738186718530.9990.02499.3
2.51-2.96.6440.02172.5810870164116360.9990.02399.7
2.9-3.556.4170.01974.4790551419141110.02199.4
3.55-5.025.6970.0272.796307111611070.9990.02299.2
5.02-37.56.2220.02175.0541816806720.9990.02398.8

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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→37.5 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.494 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: compound is maybe by-product of synthesis of 1053263; has swapped N and C atoms with C-atom carrying methyl group; N atom engages in H-bond with water; two conformations of ligand present;
RfactorNum. reflection% reflectionSelection details
Rfree0.2114 2501 5 %RANDOM
Rwork0.1857 ---
obs0.187 47324 97.7 %-
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: 35.94 Å2 / Biso mean: 10.718 Å2 / Biso min: 4.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2---0.39 Å20 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 1.12→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 59 166 1265
Biso mean--16.99 20.73 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021202
X-RAY DIFFRACTIONr_bond_other_d0.0030.02794
X-RAY DIFFRACTIONr_angle_refined_deg2.3592.0071633
X-RAY DIFFRACTIONr_angle_other_deg1.05131964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6015156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2822548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23615235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.556156
X-RAY DIFFRACTIONr_chiral_restr0.1280.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021313
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02225
LS refinement shellResolution: 1.122→1.152 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 139 -
Rwork0.219 2805 -
all-2944 -
obs--83.16 %

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