4QNE | pdb_00004qne

Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, in complex with NAD and IMP

• PDB DOI: https://doi.org/10.2210/pdb4QNE/pdb
• Entry: 4QNE supersedes: 4HLV

• Classification: OXIDOREDUCTASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-06-17 Released: 2014-08-06 
• Deposition Author(s): Osipiuk, J., Maltseva, N., Makowska-Grzyska, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, in complex with NAD and IMP

Osipiuk, J., Maltseva, N., Makowska-Grzyska, M., Gu, M., Anderson, W.F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 78.6 kDa 
• Atom Count: 5,409 
• Modeled Residue Count: 684 
• Deposited Residue Count: 732 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine 5'-monophosphate dehydrogenase	A, B	366	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: VC0767 EC: 1.1.1.205
UniProt
Find proteins for Q9KTW3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KTW3  Go to UniProtKB:  Q9KTW3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAJ	D [auth A], G [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
IMP	C [auth A], F [auth B]	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N
K	E [auth A], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34qne

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.334	α = 90
b = 121.334	β = 90
c = 94.47	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-06 
Deposition Author(s): Osipiuk, J., Maltseva, N., Makowska-Grzyska, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• This entry supersedes: 4HLV

Revision History  

• Version 1.0: 2014-08-06
  Type: Initial release
  
• Version 1.1: 2017-07-26
  Changes: Source and taxonomy
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description