7YA3 | pdb_00007ya3

Formate dehydrogenase from Novosphingobium sp. AP12 with NADP and Azide

• PDB DOI: https://doi.org/10.2210/pdb7YA3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Novosphingobium sp. AP12
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2022-06-27 Released: 2023-07-12 
• Deposition Author(s): Kim, S., Kim, K.-J.
• Funding Organization(s): Ministry of Science, ICT and Future Planning (MSIP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Dual cofactor specific formate dehydrogenase from Novosphingobium sp. AP12 with high activity.

Kim, S., Kim, K.-J.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 88.62 kDa 
• Atom Count: 6,051 
• Modeled Residue Count: 766 
• Deposited Residue Count: 784 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A, B	392	Novosphingobium sp. AP12	Mutation(s): 0  Gene Names: PMI02_01157 EC: 1.17.1.10

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	C [auth A], E [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
AZI (Subject of Investigation/LOI)	D [auth A], F [auth B]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.343	α = 90
b = 64.343	β = 90
c = 180.621	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Kim, S., Kim, K.-J.

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Funding Organization	Location	Grant Number
Ministry of Science, ICT and Future Planning (MSIP)	Korea, Republic Of	2021M3D3A1A01079480_2021-5

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2023-08-23
  Changes: Data collection
• Version 1.2: 2023-11-29
  Changes: Refinement description