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- PDB-6e5w: Crystal structure of human cellular retinol binding protein 3 in ... -

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Basic information

Entry
Database: PDB / ID: 6e5w
TitleCrystal structure of human cellular retinol binding protein 3 in complex with abnormal-cannabidiol (abn-CBD)
ComponentsRetinol-binding protein 5
KeywordsLIPID BINDING PROTEIN / vitamin A / retinol / abn-CBD / abnormal cannabidiol / cellular retinol-binding protein / CRBP3
Function / homology
Function and homology information


retinoid binding / retinal binding / retinol binding / fatty acid transport / fatty acid binding / extracellular exosome / nucleus / cytosol
Similarity search - Function
Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-HVD / Retinol-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 23, 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 1.4Oct 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

Downloads & links

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Assembly

Deposited unit
A: Retinol-binding protein 5
B: Retinol-binding protein 5
C: Retinol-binding protein 5
D: Retinol-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,30612
Polymers65,6794
Non-polymers1,6268
Water3,747208
1
A: Retinol-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8263
Polymers16,4201
Non-polymers4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8263
Polymers16,4201
Non-polymers4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Retinol-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8263
Polymers16,4201
Non-polymers4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Retinol-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8263
Polymers16,4201
Non-polymers4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.460, 127.510, 160.229
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 5 / Cellular retinol-binding protein III / CRBP-III / HRBPiso


Mass: 16419.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P82980
#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.: 4 / Source method: obtained synthetically / Formula: C21H30O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.2M sodium malonate, pH 5.0 20% PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: CCD / Date: Nov 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→99.8 Å / Num. obs: 27540 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.08 / Net I/σ(I): 7.2
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3005 / CC1/2: 0.8 / Rpim(I) all: 0.61 / % possible all: 99.9

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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: 1GGL

1ggl


Resolution: 2.5→99.773 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.64
RfactorNum. reflection% reflection
Rfree0.2377 1371 5 %
Rwork0.1886 --
obs0.1911 27415 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→99.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4405 0 116 208 4729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124609
X-RAY DIFFRACTIONf_angle_d1.2396218
X-RAY DIFFRACTIONf_dihedral_angle_d18.9182732
X-RAY DIFFRACTIONf_chiral_restr0.058671
X-RAY DIFFRACTIONf_plane_restr0.007786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.58940.34051350.25282493X-RAY DIFFRACTION100
2.5894-2.69310.27051390.24032589X-RAY DIFFRACTION100
2.6931-2.81570.32351250.22612543X-RAY DIFFRACTION100
2.8157-2.96410.30861330.2242583X-RAY DIFFRACTION100
2.9641-3.14990.25111400.21752594X-RAY DIFFRACTION100
3.1499-3.39310.2221330.20042591X-RAY DIFFRACTION100
3.3931-3.73450.23811320.1722607X-RAY DIFFRACTION100
3.7345-4.27490.21441410.16012599X-RAY DIFFRACTION100
4.2749-5.38590.17311340.1382676X-RAY DIFFRACTION100
5.3859-99.85220.21981590.18662769X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 37.6182 Å / Origin y: 0.2439 Å / Origin z: 18.3736 Å
111213212223313233
T0.182 Å2-0.0319 Å2-0.0298 Å2-0.1939 Å20.012 Å2--0.117 Å2
L0.1563 °20.0015 °2-0.0125 °2-0.0704 °2-0.1844 °2--1.4157 °2
S-0.0662 Å °-0.0176 Å °0.0268 Å °0.0053 Å °0.0101 Å °0.0142 Å °0.0262 Å °0.0639 Å °0.0463 Å °
Refinement TLS groupSelection details: all

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