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- PDB-4azr: Human epidermal fatty acid-binding protein (FABP5) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4azr
TitleHuman epidermal fatty acid-binding protein (FABP5) in complex with the endocannabinoid anandamide
ComponentsFATTY ACID-BINDING PROTEIN, EPIDERMAL
KeywordsLIPID BINDING PROTEIN / LIPID CARRIER PROTEIN / BETA-BARREL / BETA-CLAMSHELL / DOMAIN SWAPPING
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 / retrograde trans-synaptic signaling by endocannabinoid / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of D-glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin ...regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / retrograde trans-synaptic signaling by endocannabinoid / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of D-glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / long-chain fatty acid transmembrane transporter activity / Signaling by Retinoic Acid / Triglyceride catabolism / postsynaptic cytosol / epidermis development / postsynaptic density, intracellular component / long-chain fatty acid transport / 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 / synapse / lipid binding / Neutrophil degranulation / glutamatergic synapse / 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 beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-(2-hydroxyethyl)icosanamide / Fatty acid-binding protein 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSanson, B. / Wang, T. / Sun, J. / Kaczocha, M. / Ojima, I. / Deutsch, D. / Li, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Crystallographic Study of Fabp5 as an Intracellular Endocannabinoid Transporter.
Authors: Sanson, B. / Wang, T. / Sun, J. / Wang, L. / Kaczocha, M. / Ojima, I. / Deutsch, D. / Li, H.
History
DepositionJun 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FATTY ACID-BINDING PROTEIN, EPIDERMAL
B: FATTY ACID-BINDING PROTEIN, EPIDERMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6545
Polymers30,9072
Non-polymers7473
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-75 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.120, 115.150, 108.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein FATTY ACID-BINDING PROTEIN, EPIDERMAL / EPIDERMAL-TYPE FATTY ACID-BINDING PROTEIN / E-FABP / FATTY ACID-BINDING PROTEIN 5 / FABP5 / ...EPIDERMAL-TYPE FATTY ACID-BINDING PROTEIN / E-FABP / FATTY ACID-BINDING PROTEIN 5 / FABP5 / PSORIASIS-ASSOCIATED FATTY ACID-BINDING PROTEIN HOMOLOG / PA-FABP


Mass: 15453.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: EPIDERMIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01469
#2: Chemical ChemComp-A9M / N-(2-hydroxyethyl)icosanamide


Mass: 355.598 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H45NO2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsADDITIONAL 3 N-TERM AMINO ACIDS, GSH, LEFT AFTER REMOVAL OF POLY-HIS TAG

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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: 3.3 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 7.5
Details: 25% PEG 3350, 0.1 M HEPES PH 7.5. FABP INCUBATED IN A SOLUTION SATURATED WITH RESPECT TO ANANDAMIDE PRIOR TO CRYSTALLIZATION. CRYPROTECTION: 25% GLYCEROL IN MOTHER LIQUOR.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2011
RadiationMonochromator: DOUBLE SILICON(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→20 Å / Num. obs: 9014 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 50.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.1
Reflection shellResolution: 2.95→3 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B56

1b56


Resolution: 2.95→20 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.856 / SU B: 37.195 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26798 449 5 %RANDOM
Rwork0.21907 ---
obs0.22161 8531 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.508 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2--1.93 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 51 32 2191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222180
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9662910
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4645268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97625.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.16715426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6341512
X-RAY DIFFRACTIONr_chiral_restr0.0770.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021566
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4561.51328
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9222150
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.43852
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3984.5760
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 33 -
Rwork0.269 631 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8069-0.23631.14374.2508-2.13358.87170.00220.14050.591-0.4109-0.2217-0.1836-0.22430.37450.21940.1294-0.02550.03370.0732-0.02230.2051-31.231-11.72110.605
24.38691.56960.46245.1822-0.36334.12610.0914-0.54320.37150.5297-0.02510.30760.0167-0.1372-0.06630.12660.02520.02070.1694-0.09850.17090.471-17.8719.572
33.9415-0.1761-1.83297.9032-0.56196.07820.050.1590.75370.3411-0.04090.4123-0.3094-0.167-0.0090.13290.0084-0.02050.1371-0.00050.2088-4.542-14.9874.302
42.29270.14851.08124.0423-0.1843.24780.02-0.03170.1969-0.0735-0.1688-0.01560.0243-0.00520.14880.0225-0.00550.02820.0947-0.03290.1215-36.602-17.65810.49
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 59
2X-RAY DIFFRACTION2A60 - 134
3X-RAY DIFFRACTION3B0 - 60
4X-RAY DIFFRACTION4B61 - 134

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