3PZ9

Native structure of endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1

• PDB DOI: https://doi.org/10.2210/pdb3PZ9/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga petrophila RKU-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-14 Released: 2011-12-28 
• Deposition Author(s): Santos, C.R., Meza, A.N., Paiva, J.H., Silva, J.C., Ruller, R., Prade, R.A., Squina, F.M., Murakami, M.T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 0.178 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 

Literature

Structural characterization of a novel hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1

Santos, C.R., Meza, A.N., Paiva, J.H., Silva, J.C., Ruller, R., Prade, R.A., Squina, F.M., Murakami, M.T.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 44.21 kDa 
• Atom Count: 3,360 
• Modelled Residue Count: 357 
• Deposited Residue Count: 383 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5	A	383	Thermotoga petrophila RKU-1	Mutation(s): 0  Gene Names: Tpet_1542 EC: 3.2.1.78
UniProt
Find proteins for A5IMX7 (Thermotoga petrophila (strain ATCC BAA-488 / DSM 13995 / JCM 10881 / RKU-1)) Explore A5IMX7  Go to UniProtKB:  A5IMX7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 0.178 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.463	α = 90
b = 83.352	β = 90
c = 92.179	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SHELX	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Santos, C.R., Meza, A.N., Paiva, J.H., Silva, J.C., Ruller, R., Prade, R.A., Squina, F.M., Murakami, M.T.

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2024-02-21
  Changes: Data collection, Database references