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- PDB-8gew: H-FABP crystal soaked in a bromo palmitic acid solution -

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Basic information

Entry
Database: PDB / ID: 8gew
TitleH-FABP crystal soaked in a bromo palmitic acid solution
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / H-FABP / Br-Palmitic acid
Function / homology
Function and homology information


positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport ...positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport / brown fat cell differentiation / cytoskeletal protein binding / cholesterol homeostasis / negative regulation of cell population proliferation / extracellular space / extracellular exosome / nucleus / cytosol
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
2-Bromopalmitic acid / OLEIC ACID / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsHoward, E. / Cousido-Siah, A. / Alvarez, A. / Espinosa, Y. / Podjarny, A. / Mitschler, A. / Carlevaro, M.
Funding support Argentina, 1items
OrganizationGrant numberCountry
National Scientific and Technical Research Council (CONICET)22920180100010 CO Argentina
CitationJournal: Proteins / Year: 2023
Title: Lipid exchange in crystal-confined fatty acid binding proteins: X-ray evidence and molecular dynamics explanation.
Authors: Alvarez, H.A. / Cousido-Siah, A. / Espinosa, Y.R. / Podjarny, A. / Carlevaro, C.M. / Howard, E.
History
DepositionMar 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Apr 17, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell
Item: _atom_site.B_iso_or_equiv / _atom_site.calc_flag ..._atom_site.B_iso_or_equiv / _atom_site.calc_flag / _atom_site.label_alt_id / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_label_alt_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _refine.aniso_B[1][3] / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_d_res_high / _refine.ls_number_reflns_R_work / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine_hist.d_res_high / _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_chi_squared

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4263
Polymers14,8081
Non-polymers6182
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.736, 54.966, 70.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fatty acid-binding protein, heart / Fatty acid-binding protein 3 / Heart-type fatty acid-binding protein / H-FABP / Mammary-derived ...Fatty acid-binding protein 3 / Heart-type fatty acid-binding protein / H-FABP / Mammary-derived growth inhibitor / MDGI / Muscle fatty acid-binding protein / M-FABP


Mass: 14807.944 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP3, FABP11, MDGI / Production host: Escherichia coli (E. coli) / References: UniProt: P05413
#2: Chemical ChemComp-J1W / 2-Bromopalmitic acid


Mass: 335.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H31BrO2
#3: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM Tris pH 7.5, 20-25% polyethylene glycol (PEG) 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.72932 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72932 Å / Relative weight: 1
ReflectionResolution: 0.97→43.41 Å / Num. obs: 77518 / % possible obs: 99.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.2
Reflection shellResolution: 0.97→0.99 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 1.7 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.97→30.47 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.581 / SU ML: 0.014 / Cross valid method: FREE R-VALUE / ESU R: 0.021 / ESU R Free: 0.022
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.153 3816 4.927 %
Rwork0.135 --
obs-77448 99.3 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 8.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.189 Å20 Å20 Å2
2---0.154 Å20 Å2
3----0.035 Å2
Refinement stepCycle: LAST / Resolution: 0.97→30.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 39 235 1310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121269
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161292
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.6731721
X-RAY DIFFRACTIONr_angle_other_deg0.7461.6183022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2535169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.0856
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85410253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021431
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02261
X-RAY DIFFRACTIONr_nbd_refined0.3810.2195
X-RAY DIFFRACTIONr_nbd_other0.1390.239
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2515
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2149
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_it0.7640.802606
X-RAY DIFFRACTIONr_mcbond_other0.7570.801606
X-RAY DIFFRACTIONr_mcangle_it1.0361.448769
X-RAY DIFFRACTIONr_mcangle_other1.0441.449770
X-RAY DIFFRACTIONr_scbond_it0.9210.993663
X-RAY DIFFRACTIONr_scbond_other0.920.993664
X-RAY DIFFRACTIONr_scangle_it1.2521.741940
X-RAY DIFFRACTIONr_scangle_other1.2521.742941
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.49432561
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.97→1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 278 -
Rwork0.245 5320 -
obs--98 %

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