9G3W | pdb_00009g3w

Human Gamma-D crystallin R36S mutant with TNB-Cystein Protein modification

• PDB DOI: https://doi.org/10.2210/pdb9G3W/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2024-07-12 Released: 2025-07-23 
• Deposition Author(s): Hill, J.A., Pulnova, Y., Yorke, B.A.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.243 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Human Gamma-D crystallin R36S mutant with TNB-Cystein Protein modification

Hill, J.A., Pulnova, Y., Yorke, B.A.

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: 46.96 kDa 
• Atom Count: 3,066 
• Modeled Residue Count: 343 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-crystallin D	A [auth X], B [auth A]	194	Homo sapiens	Mutation(s): 1  Gene Names: CRYGD, CRYG4
UniProt & NIH Common Fund Data Resources
Find proteins for P07320 (Homo sapiens) Explore P07320  Go to UniProtKB:  P07320
PHAROS:  P07320 GTEx:  ENSG00000118231

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MNB (Subject of Investigation/LOI)	C [auth X], D [auth X], E [auth X], F [auth A], G [auth A], H [auth A]	5-MERCAPTO-2-NITRO-BENZOIC ACID C7 H5 N O4 S GANZODCWZFAEGN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A [auth X], B [auth A]	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.243 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.8	α = 90
b = 83.5	β = 90
c = 100.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystFEL	data scaling
CrystFEL	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Hill, J.A., Pulnova, Y., Yorke, B.A.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release