9IIM

Structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with nicotinamide adenine dinucleotide at 2.74 A resolution.

• PDB DOI: https://doi.org/10.2210/pdb9IIM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-20 Released: 2024-07-03 
• Deposition Author(s): Viswanathan, V., Kumari, A., Singh, A., Kumar, A., Sharma, P., Chopra, S., Jeyakanthan, J., Sharma, S., Raje, C.I., Singh, T.P.
• Funding Organization(s): Science and Engineering Research Board (SERB), Indian Council of Medical Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 0.229 
• R-Value Work: 0.164 

Literature

Structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with nicotinamide adenine dinucleotide at 2.74 A resolution.

Viswanathan, V., Kumari, A., Singh, A., Kumar, A., Sharma, P., Chopra, S., Jeyakanthan, J., Sharma, S., Raje, C.I., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 155.29 kDa 
• Atom Count: 11,379 
• Modelled Residue Count: 1,364 
• Deposited Residue Count: 1,364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B [auth C], C [auth B], D	341	Acinetobacter baumannii	Mutation(s): 0  Gene Names:  epd, gap, A7M90_08740, Aba7835_13565, ABCAM1_1226, ABR2091_1144, APD17_19525, AYR68_05750, B7L45_13105, B9W25_17760, C2U32_02225, CAS83_00220, CBL15_12235, CTZ19_12640, D8O08_008145, DLI71_18430, EA706_09520, EA720_004470, EGM95_14355, F4T85_07645, FDN00_13975, FE003_13215, FJU42_18405, FJV09_11310, GSE42_06795, HBK86_03865, IAG11_16195, SAMEA4394745_03679 EC: 1.2.1
UniProt
Find proteins for A0A059ZTK9 (Acinetobacter baumannii) Explore A0A059ZTK9  Go to UniProtKB:  A0A059ZTK9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	E [auth A], G [auth C], I [auth B], K [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4 (Subject of Investigation/LOI)	F [auth A], H [auth C], J [auth B], L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 0.229 
• R-Value Work: 0.164 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.262	α = 90
b = 167.618	β = 90
c = 151.58	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Viswanathan, V., Kumari, A., Singh, A., Kumar, A., Sharma, P., Chopra, S., Jeyakanthan, J., Sharma, S., Raje, C.I., Singh, T.P.

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Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	--
Indian Council of Medical Research	India	--

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release