4NE7 | pdb_00004ne7

Crystal Structure of engineered Kumamolisin-As from Alicyclobacillus sendaiensis, Northeast Structural Genomics Consortium (NESG) Target OR367

• PDB DOI: https://doi.org/10.2210/pdb4NE7/pdb

• Classification: HYDROLASE
• Organism(s): Alicyclobacillus sendaiensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-28 Released: 2013-11-20 
• Deposition Author(s): Guan, R., Pultz, I.S., Siegel, J.B., Seetharaman, J., Kornhaber, G., Maglaqui, M., Mao, L., Xiao, R., Everett, J.K., Baker, D., Montelione, G.T., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Northeast Structural Genomics Consortium Target OR367

Guan, R., Pultz, I.S., Seetharaman, J., Kornhaber, G., Mao, L., Xiao, R., Maglaqui, M., Everett, J.K., Acton, T.B., Baker, D., Montelione, G.T.

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: 39.4 kDa 
• Atom Count: 2,682 
• Modeled Residue Count: 356 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kumamolisin-As	A	384	Alicyclobacillus sendaiensis	Mutation(s): 0  Gene Names: scpA EC: 3.4.21
UniProt
Find proteins for Q8GB88 (Alicyclobacillus sendaiensis) Explore Q8GB88  Go to UniProtKB:  Q8GB88

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.885	α = 90
b = 110.885	β = 90
c = 75.992	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-20 
Deposition Author(s): Guan, R., Pultz, I.S., Siegel, J.B., Seetharaman, J., Kornhaber, G., Maglaqui, M., Mao, L., Xiao, R., Everett, J.K., Baker, D., Montelione, G.T., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2013-11-20
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description