3F3H | pdb_00003f3h

Crystal structure and anti-tumor activity of LZ-8 from the fungus Ganoderma lucidium

• PDB DOI: https://doi.org/10.2210/pdb3F3H/pdb

• Classification: ANTITUMOR PROTEIN
• Organism(s): Ganoderma lucidum
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2008-10-30 Released: 2009-09-15 
• Deposition Author(s): Zhou, C.Z., Huang, L., He, Y.X., Bao, R., Sun, F., Liang, C., Liu, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.246 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of LZ-8 from the medicinal fungus Ganoderma lucidium

Huang, L., Sun, F., Liang, C., He, Y.X., Bao, R., Liu, L., Zhou, C.Z.

(2009) Proteins 75: 524-527

• PubMed: 19137616 
• DOI: https://doi.org/10.1002/prot.22346
• Primary Citation Related Structures: 
  3F3H

---

Organizational Affiliation: 
• Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 25.04 kDa 
• Atom Count: 1,826 
• Modeled Residue Count: 219 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunomodulatory protein Ling Zhi-8	A, B	111	Ganoderma lucidum	Mutation(s): 0
UniProt
Find proteins for P14945 (Ganoderma lucidum) Explore P14945  Go to UniProtKB:  P14945

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.246 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.19	α = 90
b = 86.99	β = 90
c = 92.13	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-15 
Deposition Author(s): Zhou, C.Z., Huang, L., He, Y.X., Bao, R., Sun, F., Liang, C., Liu, L.

Revision History  

• Version 1.0: 2009-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description