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- PDB-7jx2: Cellular retinol-binding protein 2 (CRBP2) in complex with 2-palm... -

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Basic information

Entry
Database: PDB / ID: 7jx2
TitleCellular retinol-binding protein 2 (CRBP2) in complex with 2-palmitoylglycerol
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / palmitoylglycerol / monoacylglycerol / retinol-binding protein / lipid binding
Function / homology
Function and homology information


vitamin A metabolic process / molecular carrier activity / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid 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
1,3-dihydroxypropan-2-yl hexadecanoate / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSilvaroli, J.A. / Banarjee, S. / Golczak, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK122071 United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY023948 United States
CitationJournal: J.Lipid Res. / Year: 2021
Title: Molecular basis for the interaction of cellular retinol binding protein 2 (CRBP2) with nonretinoid ligands.
Authors: Silvaroli, J.A. / Plau, J. / Adams, C.H. / Banerjee, S. / Widjaja-Adhi, M.A.K. / Blaner, W.S. / Golczak, M.
History
DepositionAug 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5262
Polymers16,1951
Non-polymers3311
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.339, 64.450, 66.580
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 2 / Cellular retinol-binding protein II / CRBP-II


Mass: 16195.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21De / References: UniProt: P50120
#2: Chemical ChemComp-VLP / 1,3-dihydroxypropan-2-yl hexadecanoate


Mass: 330.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H38O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris HCl, PEG 3350 22-28%

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→66.58 Å / Num. obs: 15466 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.072 / Rrim(I) all: 0.134 / Net I/σ(I): 8.2
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.873 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 889 / CC1/2: 0.881 / Rpim(I) all: 0.554 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BTI

6bti


Resolution: 1.8→46.31 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2555 719 4.67 %
Rwork0.2058 --
obs0.208 15383 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1111 0 23 209 1343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081161
X-RAY DIFFRACTIONf_angle_d0.7891557
X-RAY DIFFRACTIONf_dihedral_angle_d10.042164
X-RAY DIFFRACTIONf_chiral_restr0.048166
X-RAY DIFFRACTIONf_plane_restr0.003198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.940.30421380.25942874X-RAY DIFFRACTION100
1.94-2.130.271340.22562896X-RAY DIFFRACTION99
2.13-2.440.25441570.20582890X-RAY DIFFRACTION99
2.44-3.080.28451450.22492923X-RAY DIFFRACTION99
3.08-46.310.23151450.18473081X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -4.0167 Å / Origin y: -10.3064 Å / Origin z: 15.5622 Å
111213212223313233
T0.1383 Å2-0.0039 Å20.005 Å2-0.1612 Å20.0136 Å2--0.2435 Å2
L2.2358 °2-0.4939 °2-0.8538 °2-3.1755 °20.5951 °2--2.0004 °2
S0.0419 Å °0.0413 Å °-0.0455 Å °-0.1534 Å °-0.0385 Å °0.1171 Å °0.0194 Å °-0.0943 Å °-0.0137 Å °
Refinement TLS groupSelection details: all

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