8II9 | pdb_00008ii9

crystal structure of Hyp mutant from Hypoxylon sp. E7406B

• PDB DOI: https://doi.org/10.2210/pdb8II9/pdb

• Classification: TRANSFERASE
• Organism(s): Hypoxylon sp. E7406B
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-02-24 Released: 2024-02-28 
• Deposition Author(s): Gao, J., Liu, W.D., Li, Q., Han, X., Wei, H.L., Dai, Z.J., Su, L.Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.263 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: in silico

Literature

crystal structure of Hyp

Gao, J., Liu, W.D., Li, Q., Han, X., Wei, H.L., Dai, Z.J., Su, L.Q.

To be published.

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 166.67 kDa 
• Atom Count: 10,464 
• Modeled Residue Count: 1,301 
• Deposited Residue Count: 1,488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terpene synthase	A, B, C, D	372	Hypoxylon sp. E7406B	Mutation(s): 1  Gene Names: Hyp3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.263 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.848	α = 77.49
b = 86.155	β = 85.95
c = 102.173	γ = 87.72

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-28 
Deposition Author(s): Gao, J., Liu, W.D., Li, Q., Han, X., Wei, H.L., Dai, Z.J., Su, L.Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-02-28
  Type: Initial release