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- PDB-7fxa: Crystal Structure of human FABP4 in complex with 6-bromo-4-hexyl-... -

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Basic information

Entry
Database: PDB / ID: 7fxa
TitleCrystal Structure of human FABP4 in complex with 6-bromo-4-hexyl-2-oxo-1,3-dihydroquinoline-4-carboxylic 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 domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin
Similarity search - Domain/homology
Chem-QYP / 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. / Hofheinz, W. / 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)15,5694
Polymers15,0221
Non-polymers5463
Water3,063170
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)32.440, 53.568, 74.971
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-QYP / (4S)-6-bromo-4-hexyl-2-oxo-1,2,3,4-tetrahydroquinoline-4-carboxylic acid


Mass: 354.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20BrNO3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 43.27 %
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: 1.00002 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.12→37.49 Å / Num. obs: 50695 / % possible obs: 99.4 % / Redundancy: 6.15 % / Biso Wilson estimate: 13.653 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.038 / Rsym value: 0.04 / Χ2: 0.978 / Net I/σ(I): 25.25 / Num. measured all: 308581
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
1.12-1.154.6520.13710.7915971369134330.9850.15493
1.15-1.186.1040.12713.9722066362036150.9920.13999.9
1.18-1.226.0060.11614.8921142352335200.9940.12799.9
1.22-1.255.9530.10116.6320526345134480.9940.11199.9
1.25-1.296.4050.0918.7721231331633150.9960.098100
1.29-1.346.3680.07920.9220536322532250.9970.087100
1.34-1.396.1960.07222.5919165309530930.9960.07999.9
1.39-1.456.1060.06325.3218240299029870.9970.06999.9
1.45-1.516.5980.05629.0718943287228710.9980.061100
1.51-1.596.5120.04833.2717922275827520.9980.05299.8
1.59-1.676.350.04336.2816795264526450.9980.047100
1.67-1.775.9530.03938.6614859249724960.9980.043100
1.77-1.896.6020.03444.7715588236823610.9990.03799.7
1.89-2.056.4190.03148.2814102219921970.9990.03499.9
2.05-2.246.1490.03149.6512384202220140.9980.03499.6
2.24-2.515.5420.0348.510275186118540.9990.03399.6
2.51-2.896.3870.02953.8310442163816350.9990.03199.8
2.89-3.556.1170.02954.338600142214060.9990.03198.9
3.55-5.015.4010.03151.85914110910950.9980.03598.7
5.01-37.485.8080.03353.0238806806680.9980.03698.2

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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→37.48 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.627 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: bromine partially radiolyzed
RfactorNum. reflection% reflectionSelection details
Rfree0.1509 2541 5 %RANDOM
Rwork0.1351 ---
obs0.1359 47913 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 46.52 Å2 / Biso mean: 12.935 Å2 / Biso min: 5.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 1.12→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 50 170 1260
Biso mean--18.23 21.28 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021136
X-RAY DIFFRACTIONr_bond_other_d0.0010.021148
X-RAY DIFFRACTIONr_angle_refined_deg2.0211.9851542
X-RAY DIFFRACTIONr_angle_other_deg0.8123.0022620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8555148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.86124.78346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.21415222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.712156
X-RAY DIFFRACTIONr_chiral_restr0.1270.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02239
X-RAY DIFFRACTIONr_rigid_bond_restr4.85632284
X-RAY DIFFRACTIONr_sphericity_free14.96540
X-RAY DIFFRACTIONr_sphericity_bonded8.61152392
LS refinement shellResolution: 1.121→1.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.126 145 -
Rwork0.103 3038 -
all-3183 -
obs--90.97 %

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