5T57 | pdb_00005t57

Crystal Structure of a Semialdehyde dehydrogenase NAD-binding Protein from Cupriavidus necator in Complex with Calcium and NAD

• PDB DOI: https://doi.org/10.2210/pdb5T57/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cupriavidus necator N-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-08-30 Released: 2016-09-14 
• Deposition Author(s): Cook, W.J., Fedorov, A.A., Fedorov, E.V., Huang, H., Bonanno, J.B., Gerlt, J.A., Almo, S.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.203 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Semialdehyde dehydrogenase NAD-binding Protein from Cupriavidus necator in Complex with Calcium and NAD

Cook, W.J., Fedorov, A.A., Fedorov, E.V., Huang, H., Bonanno, J.B., 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: 33.26 kDa 
• Atom Count: 2,303 
• Modeled Residue Count: 276 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Semialdehyde dehydrogenase NAD-binding protein	A	296	Cupriavidus necator N-1	Mutation(s): 0  Gene Names: CNE_BB1p11570 EC: 1.1.1.421
UniProt
Find proteins for F8GV06 (Cupriavidus necator (strain ATCC 43291 / DSM 13513 / CCUG 52238 / LMG 8453 / N-1)) Explore F8GV06  Go to UniProtKB:  F8GV06

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.203 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.903	α = 90
b = 71.14	β = 90
c = 47.649	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Cook, W.J., Fedorov, A.A., Fedorov, E.V., Huang, H., Bonanno, J.B., Gerlt, J.A., Almo, S.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118303

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2016-09-21
  Changes: Database references, Structure summary
• Version 1.2: 2017-05-03
  Changes: Database references, Structure summary
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 1.5: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description