7LHJ | pdb_00007lhj

Crystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A mutant of cellular retinol binding protein II complex with 15-cis-retinal

• PDB DOI: https://doi.org/10.2210/pdb7LHJ/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-01-25 Released: 2021-02-10 
• Deposition Author(s): Ehyaei, N., Geiger, J.H., Borhan, B.
• Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 
  0.217 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.189 (Depositor) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A mutant of cellular retinol binding protein II complex with 15cis- retinal

Ehyaei, N., Geiger, J.H., Borhan, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.96 kDa 
• Atom Count: 2,512 
• Modeled Residue Count: 266 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinol-binding protein 2	A, B	133	Homo sapiens	Mutation(s): 8  Gene Names: RBP2, CRBP2
UniProt & NIH Common Fund Data Resources
Find proteins for P50120 (Homo sapiens) Explore P50120  Go to UniProtKB:  P50120
PHAROS:  P50120 GTEx:  ENSG00000114113

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET (Subject of Investigation/LOI)	E [auth A], G [auth B]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	D [auth A], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free:  0.217 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.189 (Depositor) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.923	α = 86.203
b = 36.038	β = 86.555
c = 64.026	γ = 65.059

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data scaling
PHENIX	phasing
PDB_EXTRACT	data extraction
Coot	model building
HKL-2000	data processing
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Ehyaei, N., Geiger, J.H., Borhan, B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	--

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 2.0: 2021-04-14
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation, Non-polymer description, Other, Refinement description, Structure summary
• Version 2.1: 2023-10-18
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 2.2: 2024-10-30
  Changes: Structure summary