9LM8 | pdb_00009lm8

Crystal structure of bvFP-Pfr21

• PDB DOI: https://doi.org/10.2210/pdb9LM8/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-18 Released: 2026-01-28 
• Deposition Author(s): Ding, G., Xu, Z., Cao, L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.288 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: in silico

Literature

De novo design of NIR-I/II fluorescent proteins for in vivo deep tissue imaging

Ding, G., Xu, Z., Cao, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.88 kDa 
• Atom Count: 3,054 
• Modeled Residue Count: 381 
• Deposited Residue Count: 381 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
bvFP-Pfr21	A	381	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.288 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.625	α = 102.75
b = 45.576	β = 102.06
c = 59.021	γ = 102.21

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
autoPROC	data processing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-01-28 
Deposition Author(s): Ding, G., Xu, Z., Cao, L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-01-28
  Type: Initial release