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- PDB-1o8v: The crystal structure of Echinococcus granulosus fatty-acid-bindi... -

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Basic information

Entry
Database: PDB / ID: 1o8v
TitleThe crystal structure of Echinococcus granulosus fatty-acid-binding protein 1
ComponentsFATTY ACID BINDING PROTEIN HOMOLOG
KeywordsLIPID BINDING PROTEIN / FATTY-ACID-BINDING PROTEIN / ECHINOCOCCUS GRANULOSUS / HYDATID DISEASE / FATTY-ACID TRANSPORT
Function / homology
Function and homology information


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
PALMITIC ACID / Fatty acid-binding protein homolog 1
Similarity search - Component
Biological speciesECHINOCOCCUS GRANULOSUS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJakobsson, E. / Alvite, G. / Bergfors, T. / Esteves, A. / Kleywegt, G.J.
CitationJournal: Biochim.Biophys.Acta / Year: 2003
Title: The Crystal Structure of Echinococcus Granulosus Fatty-Acid-Binding Protein 1
Authors: Jakobsson, E. / Alvite, G. / Bergfors, T. / Esteves, A. / Kleywegt, G.J.
History
DepositionDec 4, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Other / Structure summary
Category: pdbx_database_status / pdbx_entity_instance_feature ...pdbx_database_status / pdbx_entity_instance_feature / pdbx_entry_details / struct_conn
Item: _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_ligand_of_interest / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FATTY ACID BINDING PROTEIN HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3882
Polymers15,1311
Non-polymers2561
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)28.714, 54.834, 38.691
Angle α, β, γ (deg.)90.00, 100.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FATTY ACID BINDING PROTEIN HOMOLOG / FATTY ACID BINDING PROTEIN 1 / FABP1 / DF1 / EGDF1


Mass: 15131.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ACETYLATED AMINO TERMINUS, MODIFIED CYSTEINE A 63 / Source: (gene. exp.) ECHINOCOCCUS GRANULOSUS (invertebrata) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02970
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMEMBER OF THE FABP/P2/CRBP/CRABP FAMILY OF TRANSPORTERS.
Has ligand of interestY
Has protein modificationY

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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 Å3/Da / Density % sol: 37.5 %
Crystal growpH: 8.6
Details: 30% (V/V) MMEPEG 5000, 0.1 M TRIS-HCL,PH 8.6,0.1 M NAAC.
Crystal grow
*PLUS
pH: 8.3 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
230 mMTris-HCl1droppH8.3
330 %(v/v)PEG5000 MME1reservoir
40.1 MTris-HCl1reservoirpH8.6
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0038
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2001 / Details: CYLINDRICAL GRAZING INCIDENCE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0038 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 15644 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.23 % / Biso Wilson estimate: 12.69 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 35
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.066 / Mean I/σ(I) obs: 14.7 / % possible all: 98.6
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 38.1 Å / Num. measured all: 81862 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 98.6 % / Rmerge(I) obs: 0.066

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PMP CHAIN A

1pmp


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.171 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THE LAST REFINEMENT ROUND WAS DONE AGAINST ALL DATA, RFREE VALUES ARE THE LAST RECORDED
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1575 10.1 %RANDOM
Rwork0.172 ---
obs0.174 15620 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-0.48 Å2
2---0.9 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1057 0 18 143 1218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221092
X-RAY DIFFRACTIONr_bond_other_d0.0030.021029
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9881456
X-RAY DIFFRACTIONr_angle_other_deg0.77832416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0215133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021161
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02204
X-RAY DIFFRACTIONr_nbd_refined0.1870.2158
X-RAY DIFFRACTIONr_nbd_other0.2580.21185
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0770.2712
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3490.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.216 134
Rwork0.165 1114
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4

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