3M1R | pdb_00003m1r

The crystal structure of formimidoylglutamase from Bacillus subtilis subsp. subtilis str. 168

• PDB DOI: https://doi.org/10.2210/pdb3M1R/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-05 Released: 2010-03-16 
• Deposition Author(s): Tan, K., Bigelow, L., Trevino, D., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.230 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

The crystal structure of formimidoylglutamase from Bacillus subtilis subsp. subtilis str. 168

Tan, K., Bigelow, L., Buck, K., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 218.05 kDa 
• Atom Count: 15,171 
• Modeled Residue Count: 1,904 
• Deposited Residue Count: 1,932 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formimidoylglutamase	A, B, C, D, E, F	322	Bacillus subtilis	Mutation(s): 0  Gene Names: hutG, BSU39380, EE57C EC: 3.5.3.8
UniProt
Find proteins for P42068 (Bacillus subtilis (strain 168)) Explore P42068  Go to UniProtKB:  P42068

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	KA [auth E], T [auth C]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
PEG	AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], IA [auth D], JA [auth D], K [auth A], L [auth A], M [auth A], OA [auth E], PA [auth E], QA [auth E], R [auth B], S [auth B], UA [auth F], VA [auth F], WA [auth F], XA [auth F], Y [auth C], YA [auth F], Z [auth C], ZA [auth F]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA	GA [auth D], HA [auth D], I [auth A], J [auth A], MA [auth E], NA [auth E], P [auth B], Q [auth B], SA [auth F], TA [auth F], W [auth C], X [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	FA [auth D], G [auth A], H [auth A], LA [auth E], N [auth B], O [auth B], RA [auth F], U [auth C], V [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.230 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.038	α = 90
b = 118.98	β = 90
c = 123.34	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-16 
Deposition Author(s): Tan, K., Bigelow, L., Trevino, D., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary