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

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Basic information

Entry
Database: PDB / ID: 4azq
TitleMurine epidermal fatty acid-binding protein (FABP5) in complex with the endocannabinoid 2-arachidonoylglycerol
ComponentsFATTY ACID-BINDING PROTEIN, EPIDERMAL
KeywordsLIPID BINDING PROTEIN / LIPID CARRIER PROTEIN / ENDOCANNABINOID / ANANDAMIDE / 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 / 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 / regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / Triglyceride catabolism / 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 / long-chain fatty acid transmembrane transporter activity / fatty acid transport / Neutrophil degranulation / fatty acid binding / lipid metabolic process / glucose metabolic process / glucose homeostasis / positive regulation of cold-induced thermogenesis / postsynaptic density / synapse / extracellular space / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
2-hydroxy-1-(hydroxymethyl)ethyl icosanoate / Fatty acid-binding protein 5
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 14, 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 / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry
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)15,8773
Polymers15,4551
Non-polymers4222
Water1,22568
1
A: FATTY ACID-BINDING PROTEIN, EPIDERMAL
hetero molecules

A: FATTY ACID-BINDING PROTEIN, EPIDERMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7546
Polymers30,9092
Non-polymers8444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area1320 Å2
ΔGint-22.7 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.480, 79.480, 82.700
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-2035-

HOH

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Components

#1: Protein FATTY ACID-BINDING PROTEIN, EPIDERMAL / FABP5 / 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 / KERATINOCYTE LIPID-BINDING PROTEIN / PSORIASIS-ASSOCIATED FATTY ACID-BINDING PROTEIN HOMOLOG / PA-FABP


Mass: 15454.736 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: Q05816
#2: Chemical ChemComp-G2A / 2-hydroxy-1-(hydroxymethyl)ethyl icosanoate


Mass: 386.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H46O4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.4 Å3/Da / Density % sol: 49 % / 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% PEG 3350 AND 5% MPD, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K. CRYSTALS SOAKED IN THE MOTHER LIQUOR SATURATED WITH 2-ARACHIDONOYLGLYCEROL AND ...Details: 200 MM NACL, 50 MM NAAC PH 4.8, 25% PEG 3350 AND 5% MPD, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K. CRYSTALS SOAKED IN THE MOTHER LIQUOR SATURATED WITH 2-ARACHIDONOYLGLYCEROL 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 315r / 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→20 Å / Num. obs: 10920 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 51.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.9 / % 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→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.907 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25727 545 5 %RANDOM
Rwork0.21627 ---
obs0.21831 10366 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.061 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 28 68 1157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221121
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9671499
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4375141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74525.10647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7215223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.786156
X-RAY DIFFRACTIONr_chiral_restr0.0810.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02808
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_it0.6261.5679
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21921099
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0223442
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3214.5397
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→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 39 -
Rwork0.27 746 -
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)
13.4862-0.20190.28926.1596-0.91681.4910.0445-0.2607-0.02550.12410.01820.44210.0121-0.1576-0.06270.1686-0.008-0.01360.2562-0.00580.163121.640615.86218.733
25.80970.2732-0.37551.42650.07582.56050.0908-0.2981-0.2130.12540.02220.25590.21170.0104-0.1130.15160.0110.02080.11160.02370.074728.930115.91357.4197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 50
2X-RAY DIFFRACTION2A51 - 135

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