4JCM

Crystal structure of Gamma-CGTASE from Alkalophilic bacillus clarkii at 1.65 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb4JCM/pdb

• Classification: TRANSFERASE
• Organism(s): Evansella clarkii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-22 Released: 2014-02-26 
• Deposition Author(s): Wu, L., Yang, D., Zhou, J., Wu, J., Chen, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.134 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.129 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure of Gamma-Cgtase from Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution.

Wu, L., Yang, D., Li, J., Zhou, J., Wu, J.

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: 81.76 kDa 
• Atom Count: 6,106 
• Modelled Residue Count: 669 
• Deposited Residue Count: 702 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclodextrin glucanotransferase	A	702	Evansella clarkii	Mutation(s): 0  Gene Names: cgt EC: 2.4.1.19
UniProt
Find proteins for B9A1J6 (Evansella clarkii) Explore B9A1J6  Go to UniProtKB:  B9A1J6

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth A], PA [auth A], QA [auth A], RA [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	SA [auth A], TA [auth A], UA [auth A], VA [auth A], WA [auth A], XA [auth A], YA [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	U [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.134 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 205.736	α = 90
b = 205.736	β = 90
c = 43.504	γ = 120

Software Package:

Software Name	Purpose
MLPHARE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-26 
Deposition Author(s): Wu, L., Yang, D., Zhou, J., Wu, J., Chen, J.

Revision History  

• Version 1.0: 2014-02-26
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary