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- PDB-7e25: Crystal structure of human FABP7 complexed with palmitic acid -

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Basic information

Entry
Database: PDB / ID: 7.0E+25
TitleCrystal structure of human FABP7 complexed with palmitic acid
ComponentsFatty acid-binding protein, brain
KeywordsLIPID BINDING PROTEIN / fatty acid binding protein / FABP / FABP7 / hFABP7 / palmitic acid
Function / homology
Function and homology information


NOTCH3 Intracellular Domain Regulates Transcription / Triglyceride catabolism / fatty acid transport / epithelial cell proliferation / fatty acid binding / nervous system development / negative regulation of cell population proliferation / lipid binding / 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
PALMITIC ACID / Fatty acid-binding protein, brain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017R1D1A1B03033087 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Crystal structure of human brain-type fatty acid-binding protein FABP7 complexed with palmitic acid.
Authors: Nam, K.H.
History
DepositionFeb 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,3126
Polymers15,6751
Non-polymers6375
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-14 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.895, 45.356, 42.846
Angle α, β, γ (deg.)90.000, 98.790, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-368-

HOH

21A-402-

HOH

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Components

#1: Protein Fatty acid-binding protein, brain / Brain lipid-binding protein / BLBP / Brain-type fatty acid-binding protein / B-FABP / Fatty acid- ...Brain lipid-binding protein / BLBP / Brain-type fatty acid-binding protein / B-FABP / Fatty acid-binding protein 7 / Mammary-derived growth inhibitor related


Mass: 15674.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP7, BLBP, FABPB, MRG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15540
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris-HCl, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 22336 / % possible obs: 96.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.052 / Net I/σ(I): 31.76
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.71 / Num. unique obs: 1854 / Rpim(I) all: 0.215 / % possible all: 81

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FE3

1fe3


Resolution: 1.6→30.35 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1977 1999 8.96 %
Rwork0.1731 20314 -
obs0.1754 22313 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.74 Å2 / Biso mean: 26.2015 Å2 / Biso min: 7.3 Å2
Refinement stepCycle: final / Resolution: 1.6→30.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1098 0 39 169 1306
Biso mean--40.73 37.08 -
Num. residues----139
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.30341120.22931140125277
1.64-1.680.23961380.20911402154094
1.68-1.730.2171440.20341466161097
1.73-1.790.23451430.20561459160298
1.79-1.850.21851440.18791455159998
1.85-1.930.19581430.17781450159398
1.93-2.020.2191450.17141478162398
2.02-2.120.19791460.17061485163198
2.12-2.250.18931440.17671472161698
2.25-2.430.22811470.18351493164099
2.43-2.670.19041480.19161501164999
2.67-3.060.23851490.17551513166299
3.06-3.850.18241470.1491500164799
3.85-30.350.15671490.16081500164996

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