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- PDB-7fz3: Crystal Structure of human FABP4 in complex with 4-(4-chloropheno... -

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Basic information

Entry
Database: PDB / ID: 7fz3
TitleCrystal Structure of human FABP4 in complex with 4-(4-chlorophenoxy)benzenesulfinic acid:sodium hydride
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-WDO / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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)15,5766
Polymers15,0221
Non-polymers5545
Water3,531196
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)32.653, 54.070, 75.261
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-WDO / 1-[bis(oxidanyl)-$l^{3}-sulfanyl]-4-(4-chloranylphenoxy)benzene


Mass: 269.724 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10ClO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
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: 0.70003 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70003 Å / Relative weight: 1
ReflectionResolution: 1.1→37.63 Å / Num. obs: 54965 / % possible obs: 99.9 % / Redundancy: 6.52 % / Biso Wilson estimate: 15.561 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.057 / Rsym value: 0.05 / Χ2: 0.841 / Net I/σ(I): 15.24 / Num. measured all: 356787 / Scaling rejects: 42
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
1.1-1.136.0991.2721.4924652405040420.6021.39199.8
1.13-1.166.4810.9692.0225238390238940.7421.05499.8
1.16-1.196.7240.7982.5325289376637610.8160.86699.9
1.19-1.236.6440.6882.9324616371137050.8630.74799.8
1.23-1.276.550.5553.5123385357535700.9130.60399.9
1.27-1.316.3970.4634.1722313349634880.930.50599.8
1.31-1.366.130.3655.1320589336233590.9480.39999.9
1.36-1.426.8160.3096.4422058323932360.9630.33599.9
1.42-1.486.7690.2278.5120882308530850.980.247100
1.48-1.566.6980.16811.0219995298629850.990.182100
1.56-1.646.5760.11615.1318688284328420.9950.126100
1.64-1.746.1490.08918.6216423267126710.9960.098100
1.74-1.866.8420.06825.317448255225500.9980.07499.9
1.86-2.016.8060.04735.1216021235523540.9990.051100
2.01-2.26.5850.03842.5214402219021870.9990.04199.9
2.2-2.466.0370.03346.312087200320020.9990.036100
2.46-2.846.4330.02954.5311373177117680.9990.03199.8
2.84-3.486.5510.02364.819945151915180.9990.02599.9
3.48-4.925.8960.0197071221215120810.02199.4
4.92-37.635.9350.01969.15426172471810.02199.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.7.0018refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.1→37.63 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.135 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1859 2702 5.1 %RANDOM
Rwork0.1477 ---
obs0.1497 50136 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.63 Å2 / Biso mean: 16.66 Å2 / Biso min: 7.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 1.1→37.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 42 197 1285
Biso mean--23.14 27.7 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191149
X-RAY DIFFRACTIONr_bond_other_d0.0010.021142
X-RAY DIFFRACTIONr_angle_refined_deg2.1971.9811556
X-RAY DIFFRACTIONr_angle_other_deg0.8733.0022607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15925.10249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16115225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.498156
X-RAY DIFFRACTIONr_chiral_restr0.1220.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021276
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02245
X-RAY DIFFRACTIONr_rigid_bond_restr5.06332291
X-RAY DIFFRACTIONr_sphericity_free20.915552
X-RAY DIFFRACTIONr_sphericity_bonded11.68952414
LS refinement shellResolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 178 -
Rwork0.321 3443 -
all-3621 -
obs--89.65 %

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