4IG4 | pdb_00004ig4

Crystal structure of single mutant thermostable NPPase (N86S) from Geobacillus stearothermophilus

• PDB DOI: https://doi.org/10.2210/pdb4IG4/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-12-16 Released: 2013-12-18 
• Deposition Author(s): Guo, Z., Wang, F., Huang, J., Qiu, R., Yang, Z., Wang, Y., Gong, W., Ji, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of thermostable NPPase from Geobacillus stearothermophilus

Guo, Z., Wang, F., Huang, J., Qiu, R., Yang, Z., Wang, Y., Ji, C.

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)

Macromolecule Content 

• Total Structure Weight: 59.33 kDa 
• Atom Count: 4,018 
• Modeled Residue Count: 502 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermostable NPPase	A, B	267	Geobacillus stearothermophilus	Mutation(s): 1
UniProt
Find proteins for Q8L1N9 (Geobacillus stearothermophilus) Explore Q8L1N9  Go to UniProtKB:  Q8L1N9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.822	α = 90
b = 83.287	β = 90
c = 176.024	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-18 
Deposition Author(s): Guo, Z., Wang, F., Huang, J., Qiu, R., Yang, Z., Wang, Y., Gong, W., Ji, C.

Revision History  

• Version 1.0: 2013-12-18
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description