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

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Basic information

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


vitamin A metabolic process / 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-VL7 / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3500019371 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 25, 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)33,1004
Polymers32,3902
Non-polymers7092
Water12,629701
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5502
Polymers16,1951
Non-polymers3551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5502
Polymers16,1951
Non-polymers3551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.720, 67.659, 88.780
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

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
11ARGARGPHEPHE(chain A and (resseq 2:16 or resseq 18:30 or resseq...AA2 - 163 - 17
12GLYGLYARGARG(chain A and (resseq 2:16 or resseq 18:30 or resseq...AA18 - 3019 - 31
13ILEILEVALVAL(chain A and (resseq 2:16 or resseq 18:30 or resseq...AA32 - 3433 - 35
14THRTHRTHRTHR(chain A and (resseq 2:16 or resseq 18:30 or resseq...AA37 - 3938 - 40
15ILEILETHRTHR(chain A and (resseq 2:16 or resseq 18:30 or resseq...AA42 - 7443 - 75
16ASPASPARGARG(chain A and (resseq 2:16 or resseq 18:30 or resseq...AA78 - 8079 - 81
17VALVALLYSLYS(chain A and (resseq 2:16 or resseq 18:30 or resseq...AA82 - 9883 - 99
18LYSLYSLYSLYS(chain A and (resseq 2:16 or resseq 18:30 or resseq...AA101 - 114102 - 115
19LEULEULEULEU(chain A and (resseq 2:16 or resseq 18:30 or resseq...AA117118
110GLYGLYARGARG(chain A and (resseq 2:16 or resseq 18:30 or resseq...AA122 - 127123 - 128
111VALVALLEULEU(chain A and (resseq 2:16 or resseq 18:30 or resseq...AA129 - 134130 - 135
21ARGARGPHEPHE(chain B and (resseq 2:16 or resseq 18:30 or resseq...BB2 - 163 - 17
22GLYGLYARGARG(chain B and (resseq 2:16 or resseq 18:30 or resseq...BB18 - 3019 - 31
23ILEILEVALVAL(chain B and (resseq 2:16 or resseq 18:30 or resseq...BB32 - 3433 - 35
24THRTHRTHRTHR(chain B and (resseq 2:16 or resseq 18:30 or resseq...BB37 - 3938 - 40
25ILEILETHRTHR(chain B and (resseq 2:16 or resseq 18:30 or resseq...BB42 - 7443 - 75
26ASPASPARGARG(chain B and (resseq 2:16 or resseq 18:30 or resseq...BB78 - 8079 - 81
27VALVALLYSLYS(chain B and (resseq 2:16 or resseq 18:30 or resseq...BB82 - 9883 - 99
28LYSLYSLYSLYS(chain B and (resseq 2:16 or resseq 18:30 or resseq...BB101 - 114102 - 115
29LEULEULEULEU(chain B and (resseq 2:16 or resseq 18:30 or resseq...BB117118
210GLYGLYARGARG(chain B and (resseq 2:16 or resseq 18:30 or resseq...BB122 - 127123 - 128
211VALVALLEULEU(chain B and (resseq 2:16 or resseq 18:30 or resseq...BB129 - 134130 - 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-VL7 / 1,3-dihydroxypropan-2-yl (9Z,12Z)-octadeca-9,12-dienoate


Mass: 354.524 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H38O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 701 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
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 PILATUS 6M-F / Detector: PIXEL / Date: Nov 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.35→57.72 Å / Num. obs: 71215 / % possible obs: 93 % / Redundancy: 5.7 % / Biso Wilson estimate: 13.1889285838 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.04 / Rrim(I) all: 0.073 / Net I/σ(I): 14.1
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2776 / CC1/2: 0.921 / Rpim(I) all: 0.211 / Rrim(I) all: 0.369 / % possible all: 72.7

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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: 1.3500019371→48.3914430963 Å / SU ML: 0.0893000145194 / Cross valid method: FREE R-VALUE / σ(F): 1.34201631236 / Phase error: 12.9718810683
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.148347492109 3538 4.97154500105 %
Rwork0.116549730351 67627 -
obs0.118177218425 71165 92.4749207339 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.9991231411 Å2
Refinement stepCycle: LAST / Resolution: 1.3500019371→48.3914430963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 50 701 2998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008738199990782399
X-RAY DIFFRACTIONf_angle_d0.9618348515623221
X-RAY DIFFRACTIONf_chiral_restr0.0864472756995341
X-RAY DIFFRACTIONf_plane_restr0.0057344362488416
X-RAY DIFFRACTIONf_dihedral_angle_d24.811940708921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.350002-1.36850.2080362441551200.1513362985441990X-RAY DIFFRACTION70.6630944407
1.3685-1.3880.2003604566071330.1306055212872301X-RAY DIFFRACTION79.4645772119
1.388-1.40880.1586122069481210.1229039667842684X-RAY DIFFRACTION91.5171288744
1.4088-1.43080.1603077997181580.1122454679712724X-RAY DIFFRACTION95.08413065
1.4308-1.45420.1619687765671350.1070435774382723X-RAY DIFFRACTION94.6357615894
1.4542-1.47930.1439932440291510.1048454228492729X-RAY DIFFRACTION94.3334425156
1.4793-1.50620.148404561671400.09557391199712765X-RAY DIFFRACTION94.9967298888
1.5062-1.53520.1388702130161450.09813128907082752X-RAY DIFFRACTION94.9524745985
1.5352-1.56650.1423662933461370.09023805910042674X-RAY DIFFRACTION92.741669416
1.5665-1.60060.1317408410041130.08665754194742594X-RAY DIFFRACTION88.6378519974
1.6006-1.63780.1268788820241310.08756316278892776X-RAY DIFFRACTION95.4679802956
1.6378-1.67880.1492988916841610.09125033379872786X-RAY DIFFRACTION96.181462141
1.6788-1.72420.1332544750421330.08941283220682796X-RAY DIFFRACTION96.3486842105
1.7242-1.77490.1411993844371450.09212647851322822X-RAY DIFFRACTION96.0194174757
1.7749-1.83220.1435159154871280.1034446943622772X-RAY DIFFRACTION95.2380952381
1.8322-1.89770.1418076717481320.1038948005972505X-RAY DIFFRACTION85.6725146199
1.8977-1.97370.1473599508231380.1106055875352841X-RAY DIFFRACTION96.8465539662
1.9737-2.06350.1493936830331770.1090910541452817X-RAY DIFFRACTION96.9245710586
2.0635-2.17230.1529665268511480.1091484407142824X-RAY DIFFRACTION96.6189856957
2.1723-2.30840.1514198816881430.1121196952012817X-RAY DIFFRACTION95.6690368455
2.3084-2.48660.1416495878621570.1129454627942521X-RAY DIFFRACTION86.3870967742
2.4866-2.73680.1309466923081490.1210454906262898X-RAY DIFFRACTION97.9742765273
2.7368-3.13280.1423888775571560.1254378936952887X-RAY DIFFRACTION96.9108280255
3.1328-3.94670.1436945373531310.1209196375132685X-RAY DIFFRACTION88.6370790054
3.9467-48.390.1685913353411560.1508868314262944X-RAY DIFFRACTION93.5425467713

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