[English] 日本語
Yorodumi
- PDB-7k3i: Cellular retinol-binding protein 2 (CRBP2) in complex with 2-laur... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k3i
TitleCellular retinol-binding protein 2 (CRBP2) in complex with 2-lauroylglycerol
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / lauroylglycerol / monoacylglycerol / retinol-binding protein / lipid binding
Function / homology
Function and homology information


vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / Retinoid metabolism and transport / fatty acid 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 domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin
Similarity search - Domain/homology
1,3-dihydroxypropan-2-yl dodecanoate / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsAdams, C. / Silvaroli, 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
DepositionSep 11, 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
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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4702
Polymers16,1951
Non-polymers2741
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.269, 64.560, 67.029
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 2 / Cellular retinol-binding protein II / CRBP-II


Mass: 16195.246 Da / Num. of mol.: 1
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-VLZ / 1,3-dihydroxypropan-2-yl dodecanoate / 2-lauroylglycerol


Mass: 274.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tris/HCl Ph 8.0, PEG3350 20%-25%

-
Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.2→64.56 Å / Num. obs: 51014 / % possible obs: 98.8 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Rrim(I) all: 0.085 / Net I/σ(I): 8.4
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 0.899 / Num. unique obs: 2139 / CC1/2: 0.671 / Rpim(I) all: 0.664 / % possible all: 85.6

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JVG

7jvg


Resolution: 1.2→46.499 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 2504 4.94 %
Rwork0.1836 --
obs0.1847 50715 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→46.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 19 397 1553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071227
X-RAY DIFFRACTIONf_angle_d1.0351656
X-RAY DIFFRACTIONf_dihedral_angle_d25.131475
X-RAY DIFFRACTIONf_chiral_restr0.08177
X-RAY DIFFRACTIONf_plane_restr0.005214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.22080.3641180.33542278X-RAY DIFFRACTION85
1.2457-1.27280.30921510.28382604X-RAY DIFFRACTION98
1.2728-1.30240.29491230.27182687X-RAY DIFFRACTION99
1.3024-1.3350.27241590.25812646X-RAY DIFFRACTION99
1.3711-1.41140.26121300.24052658X-RAY DIFFRACTION99
1.4114-1.4570.25291600.23152620X-RAY DIFFRACTION98
1.457-1.5090.24861410.20972660X-RAY DIFFRACTION99
1.509-1.56950.22341420.20362722X-RAY DIFFRACTION99
1.5695-1.64090.23031330.19182695X-RAY DIFFRACTION99
1.6409-1.72740.2291150.18562749X-RAY DIFFRACTION100
1.7274-1.83560.22391370.19252709X-RAY DIFFRACTION100
1.8356-1.97740.2021960.17852746X-RAY DIFFRACTION98
1.9774-2.17640.19731640.16242711X-RAY DIFFRACTION100
2.1764-2.49130.17181470.17162769X-RAY DIFFRACTION100
2.4913-3.13870.19921330.1712801X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 4.6575 Å / Origin y: 10.8772 Å / Origin z: 15.8687 Å
111213212223313233
T0.1072 Å2-0.0045 Å2-0.0077 Å2-0.1168 Å2-0.0012 Å2--0.1085 Å2
L0.9666 °20.0696 °20.156 °2-1.656 °2-0.086 °2--1.118 °2
S0.0123 Å °0.0473 Å °0.0406 Å °-0.0593 Å °0.007 Å °-0.1009 Å °-0.0219 Å °0.09 Å °-0.0293 Å °
Refinement TLS groupSelection details: all

+
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