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- PDB-7k3i: Cellular retinol-binding protein 2 (CRBP2) in complex with 2-laur... -

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Basic information

Entry
Database: PDB / ID: 7k3i
TitleCellular retinol-binding protein 2 (CRBP2) in complex with 2-lauroylglycerol
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / lauroylglycerol / 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 dodecanoate / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsAdams, C. / Silvaroli, 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
DepositionSep 11, 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)16,4702
Polymers16,1951
Non-polymers2741
Water7,152397
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)37.269, 64.560, 67.029
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-VLZ / 1,3-dihydroxypropan-2-yl dodecanoate / 2-lauroylglycerol


Mass: 274.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tris/HCl Ph 8.0, PEG3350 20%-25%

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.2→64.56 Å / Num. obs: 51014 / % possible obs: 98.8 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Rrim(I) all: 0.085 / Net I/σ(I): 8.4
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 0.899 / Num. unique obs: 2139 / CC1/2: 0.671 / Rpim(I) all: 0.664 / % possible all: 85.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JVG

7jvg


Resolution: 1.2→46.499 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 2504 4.94 %
Rwork0.1836 --
obs0.1847 50715 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→46.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 19 397 1553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071227
X-RAY DIFFRACTIONf_angle_d1.0351656
X-RAY DIFFRACTIONf_dihedral_angle_d25.131475
X-RAY DIFFRACTIONf_chiral_restr0.08177
X-RAY DIFFRACTIONf_plane_restr0.005214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.22080.3641180.33542278X-RAY DIFFRACTION85
1.2457-1.27280.30921510.28382604X-RAY DIFFRACTION98
1.2728-1.30240.29491230.27182687X-RAY DIFFRACTION99
1.3024-1.3350.27241590.25812646X-RAY DIFFRACTION99
1.3711-1.41140.26121300.24052658X-RAY DIFFRACTION99
1.4114-1.4570.25291600.23152620X-RAY DIFFRACTION98
1.457-1.5090.24861410.20972660X-RAY DIFFRACTION99
1.509-1.56950.22341420.20362722X-RAY DIFFRACTION99
1.5695-1.64090.23031330.19182695X-RAY DIFFRACTION99
1.6409-1.72740.2291150.18562749X-RAY DIFFRACTION100
1.7274-1.83560.22391370.19252709X-RAY DIFFRACTION100
1.8356-1.97740.2021960.17852746X-RAY DIFFRACTION98
1.9774-2.17640.19731640.16242711X-RAY DIFFRACTION100
2.1764-2.49130.17181470.17162769X-RAY DIFFRACTION100
2.4913-3.13870.19921330.1712801X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 4.6575 Å / Origin y: 10.8772 Å / Origin z: 15.8687 Å
111213212223313233
T0.1072 Å2-0.0045 Å2-0.0077 Å2-0.1168 Å2-0.0012 Å2--0.1085 Å2
L0.9666 °20.0696 °20.156 °2-1.656 °2-0.086 °2--1.118 °2
S0.0123 Å °0.0473 Å °0.0406 Å °-0.0593 Å °0.007 Å °-0.1009 Å °-0.0219 Å °0.09 Å °-0.0293 Å °
Refinement TLS groupSelection details: all

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