9H4X | pdb_00009h4x

Crystal structure of Ni2+ dependent glycerol-1-phosphate dehydrogenase AraM from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb9H4X/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2024-10-22 Released: 2025-11-05 
• Deposition Author(s): Mao, T., Pijning, T., Guskov, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.310 (Depositor), 0.311 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.248 (DCC) 

Starting Model: in silico

Literature

Crystal structure of Ni2+ dependent glycerol-1-phosphate dehydrogenase AraM from Bacillus subtilis

Mao, T., Pijning, T., Guskov, A.

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: 46.18 kDa 
• Atom Count: 3,093 
• Modeled Residue Count: 395 
• Deposited Residue Count: 414 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol-1-phosphate dehydrogenase [NAD(P)+]	A	414	Bacillus subtilis	Mutation(s): 0  Gene Names: egsA, araM, yseB, BSU28760 EC: 1.1.1.261
UniProt
Find proteins for P94527 (Bacillus subtilis (strain 168)) Explore P94527  Go to UniProtKB:  P94527

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI (Subject of Investigation/LOI)	C [auth A]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
13P (Subject of Investigation/LOI)	B [auth A]	1,3-DIHYDROXYACETONEPHOSPHATE C3 H7 O6 P GNGACRATGGDKBX-UHFFFAOYSA-N
NI (Subject of Investigation/LOI)	D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.310 (Depositor), 0.311 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.248 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.015	α = 90
b = 70.499	β = 95.51
c = 72.609	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Mao, T., Pijning, T., Guskov, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release