3PZQ | pdb_00003pzq

Structure of the hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 with maltose and glycerol

• PDB DOI: https://doi.org/10.2210/pdb3PZQ/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

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: 45.24 kDa 
• Atom Count: 3,276 
• 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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B, C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B, C, D	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.109	α = 90
b = 83.193	β = 90
c = 91.518	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-02-21
  Changes: Data collection, Database references, Structure summary