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- PDB-8ivf: FABP7 complexed with 25-HC -

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Basic information

Entry
Database: PDB / ID: 8ivf
TitleFABP7 complexed with 25-HC
ComponentsFatty acid-binding protein, brain
KeywordsLIPID BINDING PROTEIN / Complex
Function / homology
Function and homology information


NOTCH3 Intracellular Domain Regulates Transcription / Triglyceride catabolism / fatty acid transport / fatty acid binding / epithelial cell proliferation / 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
25-HYDROXYCHOLESTEROL / Fatty acid-binding protein, brain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWei, P.C. / Zhao, K. / Yin, L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Ministry of Science and Technology (MoST, China) China
CitationJournal: J.Cell Biol. / Year: 2024
Title: Fatty acid-binding proteins 3, 7, and 8 bind cholesterol and facilitate its egress from lysosomes.
Authors: Fang, X.X. / Wei, P. / Zhao, K. / Sheng, Z.C. / Song, B.L. / Yin, L. / Luo, J.
History
DepositionMar 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,6214
Polymers29,8162
Non-polymers8052
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint3 kcal/mol
Surface area13170 Å2
Unit cell
Length a, b, c (Å)34.700, 54.110, 67.240
Angle α, β, γ (deg.)90.00, 92.34, 90.00
Int Tables number4
Space group name H-MP1211

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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: 14907.897 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP7, BLBP, FABPB / Production host: Escherichia coli (E. coli) / References: UniProt: O15540
#2: Chemical ChemComp-HC3 / 25-HYDROXYCHOLESTEROL / (3BETA)-CHOLEST-5-ENE-3,25-DIOL


Mass: 402.653 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→42.14 Å / Num. obs: 13896 / % possible obs: 92.91 % / Redundancy: 19.18 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 58.48
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.043 / Num. unique obs: 748

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→42.14 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 1368 9.84 %
Rwork0.2115 --
obs0.2151 13896 92.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 58 106 2248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0272231
X-RAY DIFFRACTIONf_angle_d1.4923032
X-RAY DIFFRACTIONf_dihedral_angle_d23.186317
X-RAY DIFFRACTIONf_chiral_restr0.112350
X-RAY DIFFRACTIONf_plane_restr0.003379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.27451510.24661302X-RAY DIFFRACTION96
2.69-2.80.28141410.25111286X-RAY DIFFRACTION96
2.8-2.930.2971550.25641280X-RAY DIFFRACTION94
2.93-3.080.29541270.24321235X-RAY DIFFRACTION91
3.08-3.280.24121210.22231171X-RAY DIFFRACTION88
3.28-3.530.28211450.20911333X-RAY DIFFRACTION96
3.53-3.880.2231400.1981285X-RAY DIFFRACTION95
3.88-4.440.21841300.17751209X-RAY DIFFRACTION91
4.45-5.590.18331260.17051192X-RAY DIFFRACTION88
5.6-42.140.2561320.20691235X-RAY DIFFRACTION90

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