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- PDB-6l9o: Crystal structure of FABP7 apo -

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Basic information

Entry
Database: PDB / ID: 6l9o
TitleCrystal structure of FABP7 apo
ComponentsFatty acid-binding protein, brain
KeywordsLIPID BINDING PROTEIN / Fatty acid-binding protein
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 domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin
Similarity search - Domain/homology
Fatty acid-binding protein, brain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsWei, P.C. / Yin, L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China3187072 China
National Natural Science Foundation of China31470738 China
National Basic Research Program of China (973 Program)2014CB910103 China
CitationJournal: To Be Published
Title: Crystal structure of FABP7 apo
Authors: Wei, P.C. / Zhao, K. / Yin, L.
History
DepositionNov 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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


Theoretical massNumber of molelcules
Total (without water)15,0501
Polymers15,0501
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7150 Å2
Unit cell
Length a, b, c (Å)34.710, 56.760, 71.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 15050.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP7 / Production host: Escherichia coli (E. coli) / References: UniProt: O15540
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris 5.5 25% w/vPEG 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 315 / 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: 1.42→71.23 Å / Num. obs: 27180 / % possible obs: 99.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.7
Reflection shellResolution: 1.42→1.45 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 7670 / % possible all: 99.11

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FE3

1fe3


Resolution: 1.42→35.615 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.79
RfactorNum. reflection% reflection
Rfree0.1829 1999 7.35 %
Rwork0.1739 --
obs0.1746 27180 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.57 Å2 / Biso mean: 17.0395 Å2 / Biso min: 7.08 Å2
Refinement stepCycle: final / Resolution: 1.42→35.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 0 191 1233
Biso mean---27.82 -
Num. residues----132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4203-1.45580.25231390.2167175598
1.4558-1.49520.22141410.19741769100
1.4952-1.53920.2281390.1836174999
1.5392-1.58890.20441410.17261789100
1.5889-1.64560.1831410.17041769100
1.6456-1.71150.20791410.17421775100
1.7115-1.78940.18541410.17121778100
1.7894-1.88380.20941420.17371782100
1.8838-2.00180.18631410.15381786100
2.0018-2.15630.15741440.15741819100
2.1563-2.37330.18351440.1751804100
2.3733-2.71660.18541430.17881817100
2.7166-3.42220.18051480.17181845100
3.4222-35.6150.16291540.17511944100

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