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- PDB-6e6k: Crystal structure of human cellular retinol-binding protein 4 in ... -

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Basic information

Entry
Database: PDB / ID: 6e6k
TitleCrystal structure of human cellular retinol-binding protein 4 in complex with abnormal-cannabidiol (abn-CBD)
ComponentsRetinoid-binding protein 7
KeywordsLIPID BINDING PROTEIN / vitamin A / retinol / abn-CBD / abnormal cannabidiol
Function / homology
Function and homology information


retinal binding / retinol binding / fatty acid transport / fatty acid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-HVD / Retinoid-binding protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSilvaroli, J.A. / Banerjee, S. / Kiser, P.D. / Golczak, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY023948 United States
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Abnormal Cannabidiol Modulates Vitamin A Metabolism by Acting as a Competitive Inhibitor of CRBP1.
Authors: Silvaroli, J.A. / Widjaja-Adhi, M.A.K. / Trischman, T. / Chelstowska, S. / Horwitz, S. / Banerjee, S. / Kiser, P.D. / Blaner, W.S. / Golczak, M.
History
DepositionJul 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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: Retinoid-binding protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2092
Polymers15,8941
Non-polymers3141
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7370 Å2
Unit cell
Length a, b, c (Å)35.039, 57.390, 67.990
Angle α, β, γ (deg.)90.00, 103.67, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-463-

HOH

21A-540-

HOH

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Components

#1: Protein Retinoid-binding protein 7 / Cellular retinoic acid-binding protein 4 / CRBP4 / Cellular retinoic acid-binding protein IV / CRABP-IV


Mass: 15894.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96R05
#2: Chemical ChemComp-HVD / (1'R,2'R)-5'-methyl-6-pentyl-2'-(prop-1-en-2-yl)-1',2',3',4'-tetrahydro[1,1'-biphenyl]-2,4-diol


Mass: 314.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 41.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M NaCl, 0.1 M BisTris, pH 6.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→33.03 Å / Num. obs: 30515 / % possible obs: 95 % / Redundancy: 6.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.073 / Rrim(I) all: 0.133 / Net I/σ(I): 7.7
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1482 / CC1/2: 0.47 / Rpim(I) all: 0.49 / Rrim(I) all: 0.86 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AT8

6at8


Resolution: 1.3→33.03 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.46
RfactorNum. reflection% reflection
Rfree0.195 1454 4.77 %
Rwork0.1692 --
obs0.1704 30513 94.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→33.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 23 281 1391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081164
X-RAY DIFFRACTIONf_angle_d0.961570
X-RAY DIFFRACTIONf_dihedral_angle_d23.933436
X-RAY DIFFRACTIONf_chiral_restr0.085166
X-RAY DIFFRACTIONf_plane_restr0.006200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.34650.30661770.29552842X-RAY DIFFRACTION94
1.3465-1.40040.27171500.27022877X-RAY DIFFRACTION94
1.4004-1.46410.27131190.24842973X-RAY DIFFRACTION96
1.4641-1.54130.24451460.21642835X-RAY DIFFRACTION95
1.5413-1.63790.24631320.1932840X-RAY DIFFRACTION93
1.6379-1.76430.20541310.17852996X-RAY DIFFRACTION97
1.7643-1.94190.19841530.16442862X-RAY DIFFRACTION94
1.9419-2.22280.19041430.14962941X-RAY DIFFRACTION96
2.2228-2.80030.18241560.14722898X-RAY DIFFRACTION94
2.8003-33.04250.14331470.1342995X-RAY DIFFRACTION96

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