4WUV | pdb_00004wuv

Crystal Structure of a putative D-Mannonate oxidoreductase from Haemophilus influenza (Avi_5165, TARGET EFI-513796) with bound NAD

• PDB DOI: https://doi.org/10.2210/pdb4WUV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Haemophilus influenzae RdAW
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-03 Released: 2014-11-26 
• Deposition Author(s): Yadava, U., Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.172 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Literature

Crystal structure of a putative D-Mannonate oxidoreductase from Haemophilus influenza (Avi_5165, TARGET EFI-513796) with bound NAD

Yadava, U., Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 69.12 kDa 
• Atom Count: 4,964 
• Modeled Residue Count: 560 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-hydroxycyclohexanecarboxyl-CoA dehydrogenase	A, B	307	Haemophilus influenzae RdAW	Mutation(s): 0  Gene Names: HICG_00830

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
EDO	D [auth A], E [auth A], G [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.172 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.976	α = 90
b = 138.382	β = 90
c = 115.942	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Yadava, U., Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Advisory, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references
• Version 1.3: 2024-11-13
  Changes: Structure summary