[English] 日本語
Yorodumi
- PDB-5ljc: Crystal structure of holo human CRBP1 -

+
Open data


ID or keywords:

Loading...

-
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


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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more