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- PDB-3akm: X-ray structure of iFABP from human and rat with bound fluorescen... -

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Basic information

Entry
Database: PDB / ID: 3akm
TitleX-ray structure of iFABP from human and rat with bound fluorescent fatty acid analogue
ComponentsFatty acid-binding protein, intestinal
KeywordsTRANSPORT PROTEIN / beta barrel / ligand complex / fatty acid binding protein
Function / homology
Function and homology information


intestinal lipid absorption / apical cortex / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / Triglyceride catabolism / microvillus / fatty acid transport / fatty acid binding / fatty acid metabolic process / nucleus / cytosol
Similarity search - Function
Fatty acid-binding protein, intestinal / 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
Chem-11D / Fatty acid-binding protein, intestinal
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWielens, J. / Laguerre, A.J.K. / Parker, M.W. / Scanlon, M.J.
CitationJournal: To be Published
Title: Crystal structures of human and rat intestinal fatty acid binding proteins in complex with 11-(Dansylamino)undecanoic acid
Authors: Laguerre, A.J.K. / Wielens, J. / Parker, M.W. / Porter, C.J. / Scanlon, M.J.
History
DepositionJul 14, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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, intestinal
B: Fatty acid-binding protein, intestinal
C: Fatty acid-binding protein, intestinal
D: Fatty acid-binding protein, intestinal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,22812
Polymers60,3924
Non-polymers1,8368
Water1,910106
1
A: Fatty acid-binding protein, intestinal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5573
Polymers15,0981
Non-polymers4592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein, intestinal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5573
Polymers15,0981
Non-polymers4592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fatty acid-binding protein, intestinal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5573
Polymers15,0981
Non-polymers4592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fatty acid-binding protein, intestinal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5573
Polymers15,0981
Non-polymers4592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.020, 79.011, 63.240
Angle α, β, γ (deg.)90.00, 94.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fatty acid-binding protein, intestinal / Intestinal-type fatty acid-binding protein / I-FABP / Fatty acid-binding protein 2


Mass: 15098.044 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET45b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P12104
#2: Chemical
ChemComp-11D / 11-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)undecanoic acid / 11-(Dansylamino)undecanoic acid


Mass: 434.592 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H34N2O4S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30-34% w/v PEG 4000, 0.2M Magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 2008 / Details: mirrors
RadiationMonochromator: silicon 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.9→50.8 Å / Num. all: 39532 / Num. obs: 39319 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.12 / Net I/σ(I): 8.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5728 / Rsym value: 0.57 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IFB

3ifb


Resolution: 1.9→33.48 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.89 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27909 1968 5 %RANDOM
Rwork0.22599 37329 --
obs0.22866 37329 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.53 Å2 / Biso mean: 21.477 Å2 / Biso min: 7.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20 Å2
2---1.11 Å20 Å2
3---2.44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4233 0 124 106 4463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224421
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.975937
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8085520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69524.821224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87215809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.911528
X-RAY DIFFRACTIONr_chiral_restr0.0990.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023300
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_it0.9791.52576
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7524148
X-RAY DIFFRACTIONr_scbond_it2.59231845
X-RAY DIFFRACTIONr_scangle_it3.9944.51789
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 141 -
Rwork0.293 2763 -
all-2904 -
obs--99.42 %

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