9DFB | pdb_00009dfb

Q108K:K40L:T51V:T53C:R58A:Y19W:Q38L:Q4A:T29L mutant of hCRBPII bound to FR1V in the dark at pH 3.0

• PDB DOI: https://doi.org/10.2210/pdb9DFB/pdb

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


• Deposited: 2024-08-29 Released: 2025-09-03 
• Deposition Author(s): Bingham, C., Geiger, J.H.
• Funding Organization(s): National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.252 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Photoswitching fluorescence via a novel Trp-flap mechanism

Bingham, C., Ehyaei, N., Maity, S., Cantrell, J., Gwasdacus, J., Sheng, W., Vasileiou, C., Borhan, B., Geiger, J.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.59 kDa 
• Atom Count: 2,262 
• 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 [auth B], B [auth A]	133	Homo sapiens	Mutation(s): 9  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZFJ (Subject of Investigation/LOI)	C [auth B], E [auth A]	(4aP)-N,N-diethyl-9,9-dimethyl-7-[(1E)-prop-1-en-1-yl]-9H-fluoren-2-amine C22 H27 N UMARKYXLRJLTSK-RMKNXTFCSA-N
EDO	D [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.252 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.964	α = 85.701
b = 35.924	β = 86.873
c = 63.938	γ = 65.217

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Bingham, C., Geiger, J.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)		--

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release