3M1R

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.230
R-Value Work: 0.176
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formimidoylglutamase	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42068
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain KA [auth E] SDF format, chain T [auth C] MOL2 format, chain KA [auth E] MOL2 format, chain T [auth C]	KA [auth E], T [auth C]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain KA [auth E] Focus chain T [auth C] Interactions & Density Focus chain KA [auth E] Focus chain T [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain OA [auth E] SDF format, chain PA [auth E] SDF format, chain QA [auth E] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain UA [auth F] SDF format, chain VA [auth F] SDF format, chain WA [auth F] SDF format, chain XA [auth F] SDF format, chain Y [auth C] SDF format, chain YA [auth F] SDF format, chain Z [auth C] SDF format, chain ZA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain VA [auth F] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth F]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] EA [auth C] 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		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain R [auth B] Focus chain S [auth B] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain Z [auth C] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain R [auth B] Focus chain S [auth B] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain Z [auth C] Focus chain ZA [auth F]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain SA [auth F] SDF format, chain TA [auth F] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain TA [auth F] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C]	GA [auth D] HA [auth D] I [auth A] J [auth A] MA [auth E] 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		Interactions Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain SA [auth F] Focus chain TA [auth F] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain SA [auth F] Focus chain TA [auth F] Focus chain W [auth C] Focus chain X [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain LA [auth E] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain RA [auth F] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C]	FA [auth D] G [auth A] H [auth A] LA [auth E] N [auth B] 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		Interactions Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain LA [auth E] Focus chain N [auth B] Focus chain O [auth B] Focus chain RA [auth F] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain LA [auth E] Focus chain N [auth B] Focus chain O [auth B] Focus chain RA [auth F] Focus chain U [auth C] Focus chain V [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E 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
R-Value Work: 0.176
R-Value Observed: 0.179
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