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- PDB-7g04: Crystal Structure of human FABP5 in complex with 7-(4-chloropheny... -

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Basic information

Entry
Database: PDB / ID: 7g04
TitleCrystal Structure of human FABP5 in complex with 7-(4-chlorophenyl)-1,2,3,4-tetrahydronaphthalene-1-carboxylic acid
ComponentsFatty acid-binding protein 5
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING
Function / homology
Function and homology information


regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Signaling by Retinoic Acid / long-chain fatty acid transmembrane transporter activity ...regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Signaling by Retinoic Acid / long-chain fatty acid transmembrane transporter activity / Triglyceride catabolism / epidermis development / fatty acid transport / long-chain fatty acid transport / secretory granule membrane / fatty acid binding / lipid metabolic process / glucose metabolic process / azurophil granule lumen / glucose homeostasis / positive regulation of cold-induced thermogenesis / postsynaptic density / lipid binding / synapse / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / 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
Chem-WXZ / Fatty acid-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Canesso, 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 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

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein 5
B: Fatty acid-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4326
Polymers30,9352
Non-polymers4964
Water4,143230
1
A: Fatty acid-binding protein 5


Theoretical massNumber of molelcules
Total (without water)15,4681
Polymers15,4681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9645
Polymers15,4681
Non-polymers4964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.391, 62.906, 74.407
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fatty acid-binding protein 5 / Epidermal-type fatty acid-binding protein / E-FABP / Fatty acid-binding protein / epidermal / ...Epidermal-type fatty acid-binding protein / E-FABP / Fatty acid-binding protein / epidermal / Psoriasis-associated fatty acid-binding protein homolog / PA-FABP


Mass: 15467.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP5 / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01469

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Non-polymers , 5 types, 234 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-WXZ / (1R)-7-(4-chlorophenyl)-1,2,3,4-tetrahydronaphthalene-1-carboxylic acid


Mass: 286.753 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15ClO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 47.03 %
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: May 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→48.04 Å / Num. obs: 58462 / % possible obs: 99.6 % / Redundancy: 6.14 % / Biso Wilson estimate: 26.792 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.074 / Rsym value: 0.073 / Χ2: 0.901 / Net I/σ(I): 10.33 / Num. measured all: 386251
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
1.4-1.446.821.5021.2528480417641760.4651.626100
1.44-1.486.4761.2051.6326255406040540.6351.31199.9
1.48-1.526.9340.7672.6227680399239920.8170.829100
1.52-1.577.0680.5443.7127270385838580.8990.587100
1.57-1.626.9950.414.7226391377337730.9390.443100
1.62-1.676.8790.3275.8224724359635940.9530.35499.9
1.67-1.746.4950.247.6922922353335290.970.26199.9
1.74-1.816.9550.17710.3323537338633840.9830.19299.9
1.81-1.897.0080.13113.2822867326332630.990.141100
1.89-1.986.8510.116.9221237310131000.9940.108100
1.98-2.096.6510.08719.2919788297929750.9940.09599.9
2.09-2.216.1380.07720.4917228280928070.9950.08499.9
2.21-2.376.8040.06923.618031265126500.9950.075100
2.37-2.566.8250.06225.3216913248224780.9970.06799.8
2.56-2.86.6950.05626.8115212227622720.9970.0699.8
2.8-3.136.1660.05127.2212874209220880.9970.05699.8
3.13-3.616.6390.04630.2912242184918440.9980.0599.7
3.61-4.436.6790.04831.2310600159115870.9980.05299.7
4.43-6.265.9030.0529.447355124912460.9970.05599.8
6.26-48.046.2430.05830.2446457497440.9940.06399.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0112refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.4→48.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.217 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ligand occupancy set to 0.5 in one molecule, absent in the other stereocenter well defined as R
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 2826 5.1 %RANDOM
Rwork0.1899 ---
obs0.1914 52777 96.88 %-
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: 65.66 Å2 / Biso mean: 20.773 Å2 / Biso min: 13.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.54 Å20 Å2
3---0.51 Å2
Refinement stepCycle: final / Resolution: 1.4→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 30 230 2354
Biso mean--27.45 31.47 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022242
X-RAY DIFFRACTIONr_bond_other_d0.0010.021535
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.9783039
X-RAY DIFFRACTIONr_angle_other_deg1.12333791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2995295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87825.26395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02415447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3261513
X-RAY DIFFRACTIONr_chiral_restr0.1160.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022482
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02427
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 184 -
Rwork0.346 3393 -
all-3577 -
obs--90.03 %

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