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- PDB-4azp: Murine epidermal fatty acid-binding protein (FABP5) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4azp
TitleMurine epidermal fatty acid-binding protein (FABP5) in complex with the endocannabinoid anandamide
ComponentsFATTY ACID-BINDING PROTEIN, EPIDERMAL
KeywordsLIPID BINDING PROTEIN / LIPID CARRIER PROTEIN / 2-ARACHIDONOYLGLYCEROL BETA-BARREL / BETA-CLAMSHELL / DOMAIN SWAPPING
Function / homology
Function and homology information


Signaling by Retinoic Acid / regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / Triglyceride catabolism / 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 ...Signaling by Retinoic Acid / regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / Triglyceride catabolism / 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 / long-chain fatty acid transmembrane transporter activity / postsynaptic cytosol / postsynaptic density, intracellular component / Neutrophil degranulation / fatty acid binding / lipid metabolic process / glucose metabolic process / glucose homeostasis / positive regulation of cold-induced thermogenesis / postsynaptic density / synapse / glutamatergic synapse / extracellular space / identical protein binding / nucleus / 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 / Fatty acid binding protein 5, epidermal
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8323
Polymers15,4411
Non-polymers3912
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.710, 79.710, 83.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-2031-

HOH

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Components

#1: Protein FATTY ACID-BINDING PROTEIN, EPIDERMAL / MCG1638 / FABP5 / EPIDERMAL-TYPE FATTY ACID- BINDING PROTEIN / E-FABP / PSORIASIS-ASSOCIATED FATTY ...MCG1638 / FABP5 / EPIDERMAL-TYPE FATTY ACID- BINDING PROTEIN / E-FABP / PSORIASIS-ASSOCIATED FATTY ACID- BINDING PROTEIN HOMOLOG / PA-FABP


Mass: 15440.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Tissue: EPIDERMIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q497I3, UniProt: Q05816*PLUS
#2: Chemical ChemComp-A9M / N-(2-hydroxyethyl)icosanamide


Mass: 355.598 Da / Num. of mol.: 1 / 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.: 84 / 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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 200 MM NACL, 50 MM NAAC PH 4.8, 25% PEG3350 AND 5% MPD, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K. CRYSTALS SOAKED IN THE MOTHER LIQUOR SATURATED WITH ANANDAMIDE AND CONTAINING 25% ...Details: 200 MM NACL, 50 MM NAAC PH 4.8, 25% PEG3350 AND 5% MPD, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K. CRYSTALS SOAKED IN THE MOTHER LIQUOR SATURATED WITH ANANDAMIDE AND CONTAINING 25% GLYCEROL FOR CRYOPROTECTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 9556 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 47.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 22
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.3 / % possible all: 99.2

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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: 2.1→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.878 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23624 477 5 %RANDOM
Rwork0.19946 ---
obs0.20132 9070 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.088 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.24 Å20 Å2
2---0.49 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1039 0 26 84 1149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221091
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9631460
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4675137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83325.74547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80915210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.506155
X-RAY DIFFRACTIONr_chiral_restr0.0870.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02798
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_it0.6311.5669
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21221081
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1113422
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5434.5378
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 33 -
Rwork0.21 635 -
obs--99.11 %
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)
13.3946-1.57340.63884.4339-0.8812.15440.07240.3078-0.148-0.3856-0.0660.36650.2423-0.1674-0.00650.1539-0.03320.0090.12740.03420.132221.955610.74583.1101
22.39141.7191-0.29333.6888-0.12233.3022-0.05940.0394-0.0171-0.18340.0770.11570.0178-0.1024-0.01760.05670.0197-0.00410.01820.00520.007429.263516.586.4455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 43
2X-RAY DIFFRACTION2A44 - 135

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