4X3Z | pdb_00004x3z

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

• PDB DOI: https://doi.org/10.2210/pdb4X3Z/pdb

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


• Deposited: 2014-12-02 Released: 2014-12-10 
• Deposition Author(s): Osipiuk, J., MALTSEVA, N., KIM, Y., Mulligan, R., 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: 1.62 Å
• R-Value Free: 
  0.182 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

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

Osipiuk, J., MALTSEVA, N., KIM, Y., Mulligan, R., MAKOWSKA-GRZYSKA, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 78.82 kDa 
• Atom Count: 5,928 
• Modeled Residue Count: 690 
• 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: guaB, VC_0767 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth A], H [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
XMP	C [auth A], G [auth B]	XANTHOSINE-5'-MONOPHOSPHATE C10 H14 N4 O9 P DCTLYFZHFGENCW-UUOKFMHZSA-O
PO4	J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	E [auth A], I [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.182 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34x3z

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.262	α = 90
b = 91.262	β = 90
c = 171.214	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Osipiuk, J., MALTSEVA, N., KIM, Y., Mulligan, R., MAKOWSKA-GRZYSKA, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description