5M7H | pdb_00005m7h

Crystal structure of Bacillus subtilis EngA in complex with phosphate ion and GMPPNP

• PDB DOI: https://doi.org/10.2210/pdb5M7H/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-10-27 Released: 2017-12-20 
• Deposition Author(s): da Silveira Tome, C., Foucher, A.E., Jault, J.M., Housset, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.318 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Bacillus subtilis EngA in complex with phosphate ion and GMPPNP

da Silveira Tome, C., Foucher, A.E., Jault, J.M., Housset, D.

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: 49.58 kDa 
• Atom Count: 3,365 
• Modeled Residue Count: 421 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase Der	A	436	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: der, engA, yphC, BSU22840
UniProt
Find proteins for P50743 (Bacillus subtilis (strain 168)) Explore P50743  Go to UniProtKB:  P50743

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
PO4	B [auth A], E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.318 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.93	α = 90
b = 63.88	β = 97.34
c = 62.45	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): da Silveira Tome, C., Foucher, A.E., Jault, J.M., Housset, D.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Source and taxonomy
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description