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

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Basic information

Entry
Database: PDB / ID: 5ljb
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: 1.263 Å
Authorszanotti, G. / Valese, 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)16,1582
Polymers15,8711
Non-polymers2861
Water3,225179
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-1 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.120, 49.142, 75.801
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-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-DE3 / References: UniProt: P09455
#2: Chemical ChemComp-RTL / RETINOL


Mass: 286.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.03 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 279 K / Method: vapor diffusion / pH: 5
Details: .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 PILATUS3 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: 1.26→41.23 Å / Num. obs: 34582 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 17.5
Reflection shellResolution: 1.26→1.33 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.9 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KGL

1kgl


Resolution: 1.263→37.901 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 19.46
RfactorNum. reflection% reflectionSelection details
Rfree0.1845 3238 5.04 %Random selection
Rwork0.1641 ---
obs0.1652 34493 97.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.263→37.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 21 179 1303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111158
X-RAY DIFFRACTIONf_angle_d1.651558
X-RAY DIFFRACTIONf_dihedral_angle_d14.023450
X-RAY DIFFRACTIONf_chiral_restr0.077165
X-RAY DIFFRACTIONf_plane_restr0.007197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2633-1.28220.35831040.31632004X-RAY DIFFRACTION76
1.2822-1.30220.33461450.30572738X-RAY DIFFRACTION99
1.3022-1.32360.28491370.26272697X-RAY DIFFRACTION98
1.3236-1.34640.25851380.23452629X-RAY DIFFRACTION98
1.3464-1.37090.24031430.23512655X-RAY DIFFRACTION97
1.3709-1.39730.26541450.21942717X-RAY DIFFRACTION99
1.3973-1.42580.24091420.21612757X-RAY DIFFRACTION100
1.4258-1.45680.26741410.20522700X-RAY DIFFRACTION100
1.4568-1.49070.24111440.19832730X-RAY DIFFRACTION100
1.4907-1.5280.21531450.19252702X-RAY DIFFRACTION100
1.528-1.56930.21141460.17442704X-RAY DIFFRACTION100
1.5693-1.61550.17211470.17222754X-RAY DIFFRACTION100
1.6155-1.66760.19461420.16752692X-RAY DIFFRACTION99
1.6676-1.72720.15221480.16262689X-RAY DIFFRACTION99
1.7272-1.79630.21351440.17232662X-RAY DIFFRACTION98
1.7963-1.87810.19091400.18322650X-RAY DIFFRACTION98
1.8781-1.97710.21291370.17282609X-RAY DIFFRACTION96
1.9771-2.1010.17841430.16352697X-RAY DIFFRACTION99
2.101-2.26320.20291440.16212671X-RAY DIFFRACTION98
2.2632-2.49090.1561410.15992650X-RAY DIFFRACTION97
2.4909-2.85120.19341380.162646X-RAY DIFFRACTION97
2.8512-3.59180.19361410.14452615X-RAY DIFFRACTION97
3.5918-37.91750.12911430.13222687X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 0.6735 Å / Origin y: 0.014 Å / Origin z: -6.7867 Å
111213212223313233
T0.1206 Å2-0.0049 Å2-0.0005 Å2-0.1142 Å2-0.003 Å2--0.11 Å2
L1.4794 °20.2282 °20.4388 °2-1.7493 °21.0668 °2--1.8115 °2
S0.0217 Å °-0.0637 Å °-0.0452 Å °0.0502 Å °0.0713 Å °-0.0792 Å °0.1186 Å °0.0554 Å °0.0059 Å °
Refinement TLS groupSelection details: all

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