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

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Basic information

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


all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / Retinoid metabolism and transport / fatty acid transport ...all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / Retinoid metabolism and transport / fatty acid 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 / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PALMITIC ACID / Retinol-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.146 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

Downloads & links

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Assembly

Deposited unit
A: Retinol-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1282
Polymers15,8711
Non-polymers2561
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint1 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.340, 48.133, 77.555
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: 15871.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP1, CRBP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09455
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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 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: 279 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.146→48.13 Å / Num. obs: 37927 / % possible obs: 80.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 24.9
Reflection shellResolution: 1.146→1.21 Å / Redundancy: 2 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3.6 / % possible all: 22.4

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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: 1.146→40.897 Å / SU ML: 0.1 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.43
RfactorNum. reflection% reflectionSelection details
Rfree0.1727 3480 5.01 %Random selection
Rwork0.1518 ---
obs0.1528 37850 77.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.146→40.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 18 233 1354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081150
X-RAY DIFFRACTIONf_angle_d1.2371543
X-RAY DIFFRACTIONf_dihedral_angle_d14.022449
X-RAY DIFFRACTIONf_chiral_restr0.074164
X-RAY DIFFRACTIONf_plane_restr0.005197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.146-1.16170.213890.1988174X-RAY DIFFRACTION5
1.1617-1.17830.2109230.2022423X-RAY DIFFRACTION12
1.1783-1.19590.2235460.1956821X-RAY DIFFRACTION25
1.1959-1.21460.2224580.21481122X-RAY DIFFRACTION33
1.2146-1.23450.2913770.21341366X-RAY DIFFRACTION40
1.2345-1.25580.2188910.19491660X-RAY DIFFRACTION50
1.2558-1.27860.2143990.18841990X-RAY DIFFRACTION58
1.2786-1.30320.21821190.19932280X-RAY DIFFRACTION68
1.3032-1.32980.21541450.18412691X-RAY DIFFRACTION79
1.3298-1.35870.19381720.16233213X-RAY DIFFRACTION95
1.3587-1.39030.21931740.17383321X-RAY DIFFRACTION99
1.3903-1.42510.18961810.15983388X-RAY DIFFRACTION99
1.4251-1.46360.23441790.16443371X-RAY DIFFRACTION99
1.4636-1.50670.19951770.16333345X-RAY DIFFRACTION99
1.5067-1.55530.19491760.15923386X-RAY DIFFRACTION99
1.5553-1.61090.1661800.14553326X-RAY DIFFRACTION99
1.6109-1.67540.18341760.15043366X-RAY DIFFRACTION99
1.6754-1.75170.17851750.14613372X-RAY DIFFRACTION100
1.7517-1.8440.17591770.15413405X-RAY DIFFRACTION100
1.844-1.95960.16781700.14593305X-RAY DIFFRACTION98
1.9596-2.11090.14961710.14193353X-RAY DIFFRACTION98
2.1109-2.32330.17161690.13863214X-RAY DIFFRACTION95
2.3233-2.65940.17391770.15133380X-RAY DIFFRACTION99
2.6594-3.35030.1611770.15543362X-RAY DIFFRACTION99
3.3503-40.92290.15391820.14283331X-RAY DIFFRACTION99

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