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- PDB-5ljc: Crystal structure of holo human CRBP1 -

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Basic information

Entry
Database: PDB / ID: 5ljc
TitleCrystal structure of holo human CRBP1
ComponentsRetinol-binding protein 1
Keywordsretinol-binding protein / Retinol / Vitamin A / RBP
Function / homology
Function and homology information


Defective visual phototransduction due to LRAT loss of function / all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport ...Defective visual phototransduction due to LRAT loss of function / all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport / lipid droplet / fatty acid binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Retinol-binding protein 1 / 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 beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RETINOL / Retinol-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.433 Å
AuthorsZanotti, G. / Vallese, F. / Berni, R. / Menozzi, I.
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Structural and molecular determinants affecting the interaction of retinol with human CRBP1.
Authors: Menozzi, I. / Vallese, F. / Polverini, E. / Folli, C. / Berni, R. / Zanotti, G.
History
DepositionJul 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: Retinol-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1663
Polymers15,8561
Non-polymers3092
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-13 kcal/mol
Surface area7100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.035, 48.563, 75.748
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 1 / Cellular retinol-binding protein / CRBP / Cellular retinol-binding protein I / CRBP-I


Mass: 15856.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Position 108 was mutated in Leu. Q108L / Source: (gene. exp.) Homo sapiens (human) / Gene: RBP1, CRBP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09455
#2: Chemical ChemComp-RTL / RETINOL


Mass: 286.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 279 K / Method: vapor diffusion / pH: 5
Details: 0.2 M ammonium chloride, 0.1 M sodium acetate, 0.2 mM zinc chloride, pH 5,0, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.91881 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91881 Å / Relative weight: 1
ReflectionResolution: 1.43→40.883 Å / Num. obs: 23562 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 9.2
Reflection shellResolution: 1.43→1.51 Å / Redundancy: 3 % / Rmerge(I) obs: 0.504 / % possible all: 82.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LJB

5ljb


Resolution: 1.433→40.883 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 23.13
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 2183 4.99 %random selection
Rwork0.1793 ---
obs0.181 23559 98.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.433→40.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1102 0 22 178 1302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121183
X-RAY DIFFRACTIONf_angle_d1.7131591
X-RAY DIFFRACTIONf_dihedral_angle_d14.831469
X-RAY DIFFRACTIONf_chiral_restr0.074167
X-RAY DIFFRACTIONf_plane_restr0.007198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4326-1.46370.32591270.3022310X-RAY DIFFRACTION88
1.4637-1.49780.30111310.26862588X-RAY DIFFRACTION98
1.4978-1.53520.28561400.26572622X-RAY DIFFRACTION99
1.5352-1.57670.27561390.23322648X-RAY DIFFRACTION99
1.5767-1.62310.26751390.23012611X-RAY DIFFRACTION99
1.6231-1.67550.2711360.21532643X-RAY DIFFRACTION99
1.6755-1.73540.2181400.19972624X-RAY DIFFRACTION99
1.7354-1.80490.26071390.21272654X-RAY DIFFRACTION99
1.8049-1.88710.21761380.21242616X-RAY DIFFRACTION99
1.8871-1.98650.26841400.20562603X-RAY DIFFRACTION99
1.9865-2.1110.23451350.18042614X-RAY DIFFRACTION99
2.111-2.2740.25671310.17972622X-RAY DIFFRACTION98
2.274-2.50280.20641340.17822580X-RAY DIFFRACTION98
2.5028-2.86490.19661400.17712625X-RAY DIFFRACTION99
2.8649-3.60910.17951420.15472601X-RAY DIFFRACTION99
3.6091-40.89920.1681320.1422642X-RAY DIFFRACTION99

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