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- PDB-7jz5: Cellular retinol-binding protein 2 (CRBP2) in complex with 1-arac... -

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Basic information

Entry
Database: PDB / ID: 7jz5
TitleCellular retinol-binding protein 2 (CRBP2) in complex with 1-arachodonoyl-1-thio-glycerol
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
Chem-VPY / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.567 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
DepositionSep 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Apr 7, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 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

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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)33,1804
Polymers32,3902
Non-polymers7892
Water9,044502
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5902
Polymers16,1951
Non-polymers3951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5902
Polymers16,1951
Non-polymers3951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.816, 67.562, 89.477
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:

Ens-ID: 2

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 10:16 or resseq...AA2 - 83 - 9
12METMETPHEPHE(chain A and (resseq 2:8 or resseq 10:16 or resseq...AA10 - 1611 - 17
13GLYGLYVALVAL(chain A and (resseq 2:8 or resseq 10:16 or resseq...AA18 - 3419 - 35
14GLNGLNLYSLYS(chain A and (resseq 2:8 or resseq 10:16 or resseq...AA38 - 5039 - 51
15LYSLYSLYSLYS(chain A and (resseq 2:8 or resseq 10:16 or resseq...AA52 - 7553 - 76
16ASPASPARGARG(chain A and (resseq 2:8 or resseq 10:16 or resseq...AA78 - 8079 - 81
17VALVALGLNGLN(chain A and (resseq 2:8 or resseq 10:16 or resseq...AA82 - 9783 - 98
18LYSLYSLEULEU(chain A and (resseq 2:8 or resseq 10:16 or resseq...AA101 - 117102 - 118
19GLYGLYPHEPHE(chain A and (resseq 2:8 or resseq 10:16 or resseq...AA122 - 130123 - 131
110LYSLYSLYSLYS(chain A and (resseq 2:8 or resseq 10:16 or resseq...AA132 - 133133 - 134
21ARGARGTRPTRP(chain B and (resseq 2:8 or resseq 10:16 or resseq...BB2 - 83 - 9
22METMETPHEPHE(chain B and (resseq 2:8 or resseq 10:16 or resseq...BB10 - 1611 - 17
23GLYGLYVALVAL(chain B and (resseq 2:8 or resseq 10:16 or resseq...BB18 - 3419 - 35
24GLNGLNLYSLYS(chain B and (resseq 2:8 or resseq 10:16 or resseq...BB38 - 5039 - 51
25LYSLYSLYSLYS(chain B and (resseq 2:8 or resseq 10:16 or resseq...BB52 - 7553 - 76
26ASPASPARGARG(chain B and (resseq 2:8 or resseq 10:16 or resseq...BB78 - 8079 - 81
27VALVALGLNGLN(chain B and (resseq 2:8 or resseq 10:16 or resseq...BB82 - 9783 - 98
28LYSLYSLEULEU(chain B and (resseq 2:8 or resseq 10:16 or resseq...BB101 - 117102 - 118
29GLYGLYPHEPHE(chain B and (resseq 2:8 or resseq 10:16 or resseq...BB122 - 130123 - 131
210LYSLYSLYSLYS(chain B and (resseq 2:8 or resseq 10:16 or resseq...BB132 - 133133 - 134

NCS ensembles :
ID
1
2

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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 / Variant (production host): Bl21De / References: UniProt: P50120
#2: Chemical ChemComp-VPY / S-[(2R)-2,3-dihydroxypropyl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenethioate


Mass: 394.611 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.76 Å3/Da / Density % sol: 55.47 %
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: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.567→89.48 Å / Num. obs: 49723 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 20.7965774047 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.055 / Rrim(I) all: 0.111 / Net I/σ(I): 14.1
Reflection shellResolution: 1.57→1.59 Å / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2289 / CC1/2: 0.85 / Rpim(I) all: 0.432 / Rrim(I) all: 0.818 / % possible all: 93.8

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Processing

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

6bti


Resolution: 1.567→53.917927416 Å / SU ML: 0.153260420753 / Cross valid method: FREE R-VALUE / σ(F): 1.33783839746 / Phase error: 19.7748977951
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.183091092613 2442 4.91922162685 %
Rwork0.160562670614 47200 -
obs0.161702646311 49642 99.4231924695 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.9833594357 Å2
Refinement stepCycle: LAST / Resolution: 1.567→53.917927416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 54 502 2776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008116514717262372
X-RAY DIFFRACTIONf_angle_d1.033786775673190
X-RAY DIFFRACTIONf_chiral_restr0.0601569648423341
X-RAY DIFFRACTIONf_plane_restr0.00629531700245416
X-RAY DIFFRACTIONf_dihedral_angle_d19.67739079951434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5672-1.59920.240663122861390.2292326124452590X-RAY DIFFRACTION94.625520111
1.5992-1.63390.2528814235511290.2142461329212759X-RAY DIFFRACTION99.8962296783
1.6339-1.67190.2490792001781410.2245033189732744X-RAY DIFFRACTION99.8961218837
1.6719-1.71380.2410673294371360.1972124319282763X-RAY DIFFRACTION99.7934595525
1.7138-1.76010.2127845360221340.1889761495852777X-RAY DIFFRACTION99.8627787307
1.7601-1.81190.2270527752491540.18867142032757X-RAY DIFFRACTION99.8627787307
1.8119-1.87040.2235811771511330.1831963994652756X-RAY DIFFRACTION99.9653979239
1.8704-1.93720.2354066439491260.1884746242522804X-RAY DIFFRACTION99.8977156495
1.9372-2.01480.1835951980241350.1772760232832756X-RAY DIFFRACTION99.9308676115
2.0148-2.10650.2199115452231300.1726351813192787X-RAY DIFFRACTION99.965729952
2.1065-2.21760.1815174532991620.165926748092769X-RAY DIFFRACTION99.965893588
2.2176-2.35650.2104166216871410.1573693184552791X-RAY DIFFRACTION99.9318336742
2.3565-2.53840.1971399942951650.1574592138542772X-RAY DIFFRACTION99.7622282609
2.5384-2.79390.1911377677761390.1528054977732818X-RAY DIFFRACTION99.9324095978
2.7939-3.19810.1568249864081750.1530501568842787X-RAY DIFFRACTION99.5965030262
3.1981-4.02910.1605138897071480.1419587753462832X-RAY DIFFRACTION99.2010652463
4.0291-53.910.1545231322611550.1455838518122938X-RAY DIFFRACTION98.1593145033

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