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- PDB-6e6m: Crystal structure of human cellular retinol-binding protein 1 in ... -

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Basic information

Entry
Database: PDB / ID: 6e6m
TitleCrystal structure of human cellular retinol-binding protein 1 in complex with cannabidiorcin (CBDO)
ComponentsRetinol-binding protein 1
KeywordsLIPID BINDING PROTEIN / vitamin A / retinol / CBDO / cannabidiorcin
Function / homology
Function and homology information


all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport ...all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport / lipid droplet / fatty acid binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Retinol-binding protein 1 / 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-8CB / Retinol-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsSilvaroli, J.A. / Horwitz, S. / 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 1.1Mar 13, 2019Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Aug 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 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Retinol-binding protein 1
B: Retinol-binding protein 1
C: Retinol-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4826
Polymers49,7073
Non-polymers7753
Water13,727762
1
A: Retinol-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8272
Polymers16,5691
Non-polymers2581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8272
Polymers16,5691
Non-polymers2581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Retinol-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8272
Polymers16,5691
Non-polymers2581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.210, 93.040, 119.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Retinol-binding protein 1 / Cellular retinol-binding protein / CRBP / Cellular retinol-binding protein I / CRBP-I


Mass: 16568.869 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP1, CRBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09455
#2: Chemical ChemComp-8CB / (1'R,2'R)-4,5'-dimethyl-2'-(prop-1-en-2-yl)-1',2',3',4'-tetrahydro[1,1'-biphenyl]-2,6-diol / cannabidiorcin / CBDO


Mass: 258.355 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H22O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 762 / 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: 41.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 m BisTris, pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: CCD / Date: Mar 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.55→73.49 Å / Num. obs: 61400 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.105 / Net I/σ(I): 9
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2931 / CC1/2: 0.85 / Rpim(I) all: 0.48 / Rrim(I) all: 0.94

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.55→73.487 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.23
RfactorNum. reflection% reflection
Rfree0.2029 3000 4.91 %
Rwork0.1658 --
obs0.1676 61150 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→73.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 57 762 4171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093665
X-RAY DIFFRACTIONf_angle_d1.0024954
X-RAY DIFFRACTIONf_dihedral_angle_d14.5552217
X-RAY DIFFRACTIONf_chiral_restr0.061520
X-RAY DIFFRACTIONf_plane_restr0.006637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.57540.2791330.2392692X-RAY DIFFRACTION100
1.5754-1.60260.25911540.21692709X-RAY DIFFRACTION100
1.6026-1.63170.25991420.21322738X-RAY DIFFRACTION100
1.6317-1.66310.21831370.1982710X-RAY DIFFRACTION100
1.6631-1.69710.20811700.19122753X-RAY DIFFRACTION100
1.6971-1.7340.23221400.18772671X-RAY DIFFRACTION100
1.734-1.77430.19571320.19112795X-RAY DIFFRACTION100
1.7743-1.81870.2631470.18552734X-RAY DIFFRACTION100
1.8187-1.86790.24021280.1792764X-RAY DIFFRACTION100
1.8679-1.92280.19171490.17632730X-RAY DIFFRACTION100
1.9228-1.98490.231320.17032761X-RAY DIFFRACTION100
1.9849-2.05580.22781310.16832774X-RAY DIFFRACTION100
2.0558-2.13820.22221550.1682740X-RAY DIFFRACTION100
2.1382-2.23550.17931370.15762764X-RAY DIFFRACTION100
2.2355-2.35330.19991420.15492784X-RAY DIFFRACTION100
2.3533-2.50080.23091320.15712792X-RAY DIFFRACTION100
2.5008-2.69390.20221460.16272787X-RAY DIFFRACTION100
2.6939-2.9650.23271390.16152804X-RAY DIFFRACTION100
2.965-3.3940.15651420.15142845X-RAY DIFFRACTION100
3.394-4.27610.16061580.13872828X-RAY DIFFRACTION100
4.2761-73.56940.20931540.17322975X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -10.2363 Å / Origin y: -4.3617 Å / Origin z: 9.5237 Å
111213212223313233
T0.1382 Å2-0.0013 Å20.0026 Å2-0.1369 Å2-0.0158 Å2--0.1405 Å2
L0.2031 °2-0.0522 °2-0.0149 °2-0.168 °20.0056 °2--0.0014 °2
S0.0058 Å °-0.0188 Å °0.0473 Å °0.0154 Å °0.004 Å °-0.0027 Å °-0.0207 Å °-0.0079 Å °-0 Å °
Refinement TLS groupSelection details: all

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