4DFS | pdb_00004dfs

Structure of the catalytic domain of an endo-1,3-beta-glucanase (laminarinase) from Thermotoga petrophila RKU-1

• PDB DOI: https://doi.org/10.2210/pdb4DFS/pdb

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


• Deposited: 2012-01-24 Released: 2012-03-14 
• Deposition Author(s): Meza, A.N., Ruller, R., Prade, R.A., Squina, F.M., Santos, C.R., Murakami, M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.75 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Structural studies of an endo-1,3-beta-glucanase from Thermotoga petrophila RKU-1

Meza, A.N., Ruller, R., Prade, R.A., Squina, F.M., Santos, C.R., 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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 61.53 kDa 
• Atom Count: 4,113 
• Modeled Residue Count: 504 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase, family 16	A, B	267	Thermotoga petrophila RKU-1	Mutation(s): 0  Gene Names: Tpet_0899
UniProt
Find proteins for A5IL44 (Thermotoga petrophila (strain ATCC BAA-488 / DSM 13995 / JCM 10881 / RKU-1)) Explore A5IL44  Go to UniProtKB:  A5IL44

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	C [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.75 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.036	α = 90
b = 130.036	β = 90
c = 141.466	γ = 120

Software Package:

Software Name	Purpose
NatXray	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-14 
Deposition Author(s): Meza, A.N., Ruller, R., Prade, R.A., Squina, F.M., Santos, C.R., Murakami, M.T.

Revision History  

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description