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- PDB-7fya: Crystal Structure of apo human FABP1 - orthorhombic form -

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Basic information

Entry
Database: PDB / ID: 7fya
TitleCrystal Structure of apo human FABP1 - orthorhombic form
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING
Function / homology
Function and homology information


response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism ...response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism / antioxidant activity / peroxisomal matrix / fatty acid transport / Regulation of lipid metabolism by PPARalpha / : / fatty acid binding / PPARA activates gene expression / Cytoprotection by HMOX1 / phospholipid binding / cellular response to hydrogen peroxide / cellular response to hypoxia / chromatin binding / negative regulation of apoptotic process / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Lipocalin / cytosolic fatty-acid binding protein family / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin
Similarity search - Domain/homology
Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To be published
Title: Crystal Structure of human FABP1
Authors: Obst, U. / Magnone, C. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein, liver
B: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)29,0172
Polymers29,0172
Non-polymers00
Water2,288127
1
A: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)14,5091
Polymers14,5091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)14,5091
Polymers14,5091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.738, 56.431, 110.998
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Fatty acid-binding protein, liver / Fatty acid-binding protein 1 / Liver-type fatty acid-binding protein / L-FABP


Mass: 14508.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP1, FABPL / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07148
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→39.57 Å / Num. obs: 19160 / % possible obs: 93.2 % / Redundancy: 4.84 % / Biso Wilson estimate: 32.69 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 17.76 / Num. measured all: 119049
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. possibleNum. unique obsNet I/σ(I) obs% possible all
1.88-1.933.290.78712319521.2677.3
1.93-1.983.340.664138211121.680.5
1.98-2.033.850.519129110752.2683.3
2.03-2.084.080.44311489913.1186.3
2.08-2.144.080.376123910833.8987.4
2.14-2.24.220.299111210064.990.5
2.2-2.274.210.277116810785.8892.3
2.27-2.344.290.24310059666.0696.1
2.34-2.424.50.18710309997.8997
2.42-2.525.210.157110610709.8196.7
2.52-2.635.510.1181039103212.7599.3
2.63-2.765.920.0971029102716.6399.8
2.76-2.916.060.07596396021.3299.7
2.91-3.15.590.0697397026.3399.7
3.1-3.356.230.04597997835.499.9
3.35-3.76.180.03896096043.01100
3.7-4.265.830.03697096946.599.9
4.26-5.445.840.0397497149.5899.7
5.44-39.575.570.02696996148.5999.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_989refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.88→36.575 Å / FOM work R set: 0.7637 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2739 981 5.12 %RANDOM
Rwork0.2152 18171 --
obs0.2181 19152 93.32 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.579 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 73.91 Å2 / Biso mean: 35.81 Å2 / Biso min: 21.88 Å2
Baniso -1Baniso -2Baniso -3
1--5.4864 Å2-0 Å20 Å2
2---4.7715 Å20 Å2
3---10.2579 Å2
Refinement stepCycle: final / Resolution: 1.88→36.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 0 127 2153
Biso mean---37.5 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072057
X-RAY DIFFRACTIONf_angle_d1.1052752
X-RAY DIFFRACTIONf_chiral_restr0.075321
X-RAY DIFFRACTIONf_plane_restr0.004349
X-RAY DIFFRACTIONf_dihedral_angle_d16.138786
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.88-1.97910.36641230.30862137226079
1.9791-2.10310.32051320.27192332246485
2.1031-2.26550.33851360.25772509264591
2.2655-2.49340.31831530.26762646279997
2.4934-2.85410.34061500.254827662916100
2.8541-3.59540.27231500.208128132963100
3.5954-36.58150.21111370.177929683105100

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