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

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Basic information

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


vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / Retinoid metabolism and transport / 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 / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin
Similarity search - Domain/homology
1,3-dihydroxypropan-2-yl (9Z)-octadec-9-enoate / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.30000068656 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinol-binding protein 2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1044
Polymers32,3902
Non-polymers7132
Water11,061614
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5522
Polymers16,1951
Non-polymers3571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5522
Polymers16,1951
Non-polymers3571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.099, 67.380, 87.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGTRPTRP(chain A and (resseq 2:8 or resseq 13:16 or resseq...AA2 - 83 - 9
12ASNASNPHEPHE(chain A and (resseq 2:8 or resseq 13:16 or resseq...AA13 - 1614 - 17
13TYRTYRASPASP(chain A and (resseq 2:8 or resseq 13:16 or resseq...AA19 - 2620 - 27
14THRTHRLEULEU(chain A and (resseq 2:8 or resseq 13:16 or resseq...AA29 - 3630 - 37
15GLNGLNSERSER(chain A and (resseq 2:8 or resseq 13:16 or resseq...AA38 - 5539 - 56
16PHEPHEPHEPHE(chain A and (resseq 2:8 or resseq 13:16 or resseq...AA5758
17TYRTYRTHRTHR(chain A and (resseq 2:8 or resseq 13:16 or resseq...AA60 - 7461 - 75
18ASPASPARGARG(chain A and (resseq 2:8 or resseq 13:16 or resseq...AA78 - 8079 - 81
19VALVALLYSLYS(chain A and (resseq 2:8 or resseq 13:16 or resseq...AA82 - 9883 - 99
110LYSLYSGLUGLU(chain A and (resseq 2:8 or resseq 13:16 or resseq...AA101 - 102102 - 103
111GLYGLYASPASP(chain A and (resseq 2:8 or resseq 13:16 or resseq...AA105 - 113106 - 114
112LEULEULEULEU(chain A and (resseq 2:8 or resseq 13:16 or resseq...AA117118
113GLYGLYLEULEU(chain A and (resseq 2:8 or resseq 13:16 or resseq...AA122 - 134123 - 135
21ARGARGTRPTRP(chain B and (resseq 2:8 or resseq 13:16 or resseq...BB2 - 83 - 9
22ASNASNPHEPHE(chain B and (resseq 2:8 or resseq 13:16 or resseq...BB13 - 1614 - 17
23TYRTYRASPASP(chain B and (resseq 2:8 or resseq 13:16 or resseq...BB19 - 2620 - 27
24THRTHRLEULEU(chain B and (resseq 2:8 or resseq 13:16 or resseq...BB29 - 3630 - 37
25GLNGLNSERSER(chain B and (resseq 2:8 or resseq 13:16 or resseq...BB38 - 5539 - 56
26PHEPHEPHEPHE(chain B and (resseq 2:8 or resseq 13:16 or resseq...BB5758
27TYRTYRTHRTHR(chain B and (resseq 2:8 or resseq 13:16 or resseq...BB60 - 7461 - 75
28ASPASPARGARG(chain B and (resseq 2:8 or resseq 13:16 or resseq...BB78 - 8079 - 81
29VALVALLYSLYS(chain B and (resseq 2:8 or resseq 13:16 or resseq...BB82 - 9883 - 99
210LYSLYSGLUGLU(chain B and (resseq 2:8 or resseq 13:16 or resseq...BB101 - 102102 - 103
211GLYGLYASPASP(chain B and (resseq 2:8 or resseq 13:16 or resseq...BB105 - 113106 - 114
212LEULEULEULEU(chain B and (resseq 2:8 or resseq 13:16 or resseq...BB117118
213GLYGLYLEULEU(chain B and (resseq 2:8 or resseq 13:16 or resseq...BB122 - 134123 - 135

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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.: 2
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-YOG / 1,3-dihydroxypropan-2-yl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris HCl, PEG 3350 22-28% / PH range: 7.5 - 8.5

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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 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.3→67.38 Å / Num. obs: 83038 / % possible obs: 97.3 % / Redundancy: 5.8 % / Biso Wilson estimate: 15.0553468257 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.046 / Rrim(I) all: 0.084 / Net I/σ(I): 10.9
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3342 / CC1/2: 0.627 / Rpim(I) all: 0.597 / Rrim(I) all: 0.993 / % possible all: 80.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BTI

6bti


Resolution: 1.30000068656→48.4853656136 Å / SU ML: 0.120325564302 / Cross valid method: FREE R-VALUE / σ(F): 1.33958163152 / Phase error: 17.7273561695
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1738 4199 5.06214662021 %
Rwork0.1335 78750 -
obs0.135588207009 82949 96.961939496 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.4291838733 Å2
Refinement stepCycle: LAST / Resolution: 1.30000068656→48.4853656136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 50 614 2918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008827544316362457
X-RAY DIFFRACTIONf_angle_d0.9765094427383309
X-RAY DIFFRACTIONf_chiral_restr0.085719896757351
X-RAY DIFFRACTIONf_plane_restr0.0058934931945428
X-RAY DIFFRACTIONf_dihedral_angle_d23.4688768352946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3000007-1.31480.3429948189991060.3245847445072124X-RAY DIFFRACTION78.7707523843
1.3148-1.33020.2916462197851040.292248X-RAY DIFFRACTION83.9100963254
1.3302-1.34650.2775001134481310.2750861327452364X-RAY DIFFRACTION88.2873319179
1.3465-1.36350.2481609698941310.2385536940882487X-RAY DIFFRACTION93.9024390244
1.3635-1.38150.2317132794311330.2125347283762538X-RAY DIFFRACTION94.7163120567
1.3815-1.40040.2088565223841330.1993305161122591X-RAY DIFFRACTION96.3565617262
1.4004-1.42040.2359670153161430.1821400338992602X-RAY DIFFRACTION96.8253968254
1.4204-1.44160.2477916301821260.1677419723742640X-RAY DIFFRACTION98.4341637011
1.4416-1.46410.1748654249891470.1647862804932631X-RAY DIFFRACTION98.3014861996
1.4641-1.48810.2200960341191370.151084414762661X-RAY DIFFRACTION98.3134223472
1.4881-1.51380.1812319994081320.1387017319172653X-RAY DIFFRACTION99.039829303
1.5138-1.54130.1723507889491530.1349008233982619X-RAY DIFFRACTION98.0891719745
1.5413-1.5710.1600498395281480.1207989914362646X-RAY DIFFRACTION98.623367455
1.571-1.6030.1580489339381350.1083588397822694X-RAY DIFFRACTION99.507562434
1.603-1.63790.1482203682831310.1053965455832648X-RAY DIFFRACTION98.896797153
1.6379-1.6760.1789273319831450.1079943241712662X-RAY DIFFRACTION99.1872791519
1.676-1.71790.1536766641871370.1062157356432675X-RAY DIFFRACTION99.2937853107
1.7179-1.76440.13288310421460.1052339622932703X-RAY DIFFRACTION99.3028929941
1.7644-1.81630.1435190571761450.115729751372661X-RAY DIFFRACTION98.6291739895
1.8163-1.87490.1649774801311580.1156676366172657X-RAY DIFFRACTION99.3997175141
1.8749-1.94190.1632767614691420.1146968601432688X-RAY DIFFRACTION99.4028802248
1.9419-2.01970.1392053039691650.1136766300862664X-RAY DIFFRACTION99.3677555321
2.0197-2.11160.1447910738051740.1119553983512681X-RAY DIFFRACTION99.5467224547
2.1116-2.22290.1617797391971360.1096065634652697X-RAY DIFFRACTION99.3338008415
2.2229-2.36220.146653546391410.1167499554672667X-RAY DIFFRACTION97.9079497908
2.3622-2.54460.1688185324291360.1270378316442739X-RAY DIFFRACTION99.722511273
2.5446-2.80060.181773682521430.1391645712052742X-RAY DIFFRACTION99.7579529737
2.8006-3.20580.2046843969241580.1362294645032761X-RAY DIFFRACTION99.6585865483
3.2058-4.03870.1670970246951270.1219371379252727X-RAY DIFFRACTION97.3065121036

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