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- PDB-6i8x: As-p18, an extracellular fatty acid binding protein -

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Basic information

Entry
Database: PDB / ID: 6i8x
TitleAs-p18, an extracellular fatty acid binding protein
ComponentsFatty acid-binding protein homolog
KeywordsLIPID BINDING PROTEIN / Extracellular / nematodes / fatty acid binding
Function / homology
Function and homology information


Fatty acid-binding protein homologue 1/2/3/4 / Cytosolic fatty-acid binding proteins signature. / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
VACCENIC ACID / Fatty acid-binding protein homolog
Similarity search - Component
Biological speciesAscaris suum (pig roundworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGabrielsen, M. / Riboldi-Tunnicliffe, A. / Ibanez-Shimabukuro, M. / Smith, B.O.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust083625 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/G011389/1 United Kingdom
Citation
Journal: Biosci.Rep. / Year: 2019
Title: As-p18, an extracellular fatty acid binding protein of nematodes, exhibits unusual structural features.
Authors: Ibanez-Shimabukuro, M. / Rey-Burusco, M.F. / Gabrielsen, M. / Franchini, G.R. / Riboldi-Tunnicliffe, A. / Roe, A.J. / Griffiths, K. / Cooper, A. / Corsico, B. / Kennedy, M.W. / Smith, B.O.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2012

Title: Useable diffraction data from a multiple microdomain-containing crystal of Ascaris suum As-p18 fatty-acid-binding protein using a microfocus beamline.
Authors: Gabrielsen, M. / Riboldi-Tunnicliffe, A. / Ibanez-Shimabukuro, M. / Griffiths, K. / Roe, A.J. / Cooper, A. / Smith, B.O. / Corsico, B. / Kennedy, M.W.
History
DepositionNov 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein homolog
B: Fatty acid-binding protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,66314
Polymers35,2762
Non-polymers1,38812
Water1,928107
1
A: Fatty acid-binding protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,68111
Polymers17,6381
Non-polymers1,04310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9823
Polymers17,6381
Non-polymers3452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.254, 102.254, 103.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Fatty acid-binding protein homolog / AS-P18


Mass: 17637.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ascaris suum (pig roundworm)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P55776
#2: Chemical ChemComp-VCA / VACCENIC ACID / (11E)-OCTADEC-11-ENOIC ACID / Vaccenic acid


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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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: 3.97 Å3/Da / Density % sol: 69.03 % / Description: Square cuboid
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 40% ethylene glycol, 0.1 M acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.3→20.06 Å / Num. obs: 23648 / % possible obs: 93.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 49.52 Å2 / Rpim(I) all: 0.049 / Rrim(I) all: 0.104 / Net I/σ(I): 9.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.8 / Rpim(I) all: 0.435 / Rrim(I) all: 0.679 / % possible all: 77.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G74
Resolution: 2.3→14.41 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.184 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.171
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1199 5.16 %RANDOM
Rwork0.179 ---
obs0.181 23252 98.6 %-
Displacement parametersBiso mean: 47.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.0353 Å20 Å20 Å2
2---1.0353 Å20 Å2
3---2.0706 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2.3→14.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 94 107 2637
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012733HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.073775HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d987SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes362HARMONIC5
X-RAY DIFFRACTIONt_it2733HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.62
X-RAY DIFFRACTIONt_other_torsion19.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion312SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2815SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.234 155 5.99 %
Rwork0.217 2432 -
all0.218 2587 -
obs--89.05 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.441-0.01380.75680.5378-0.22161.5142-0.0517-0.11150.18340.05470.01420.0276-0.21530.00960.0375-0.0113-0.0243-0.0025-0.0491-0.0544-0.10356.959726.525856.8608
21.6433-0.52670.0731.01680.21931.81270.06980.09970.1328-0.1682-0.0338-0.0439-0.28880.0549-0.0360.0068-0.03870.0382-0.05780.053-0.119414.391322.807229.0953
31.52221.7040.48772.9827-0.29041.80570.0104-0.0676-0.0314-0.0354-0.0133-0.0080.0509-0.07760.00290.1722-0.0672-0.06330.14590.00680.19219.633122.890242.5412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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