6ZCV | pdb_00006zcv

Crystal structure of lanthanide-dependent alcohol dehydrogenase PedH from Pseudomonas putida KT2440

• PDB DOI: https://doi.org/10.2210/pdb6ZCV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-06-12 Released: 2020-07-15 
• Deposition Author(s): Bange, G., Lepak, A., Elsayed, E.M.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.160 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Starting Model: experimental

Literature

Engineered PQQ-Dependent Alcohol Dehydrogenase for the Oxidation of 5-(Hydroxymethyl)furoic Acid

Wehrmann, M., Elsayed, E.M., Koebbing, S., Bendz, L., Lepak, A., Schwabe, J., Wierckx, N., Bange, G., Klebensberger, J.

(2020) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.0c01789

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 66.22 kDa 
• Atom Count: 4,958 
• Modeled Residue Count: 562 
• Deposited Residue Count: 601 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Quinoprotein ethanol dehydrogenase	A	601	Pseudomonas putida KT2440	Mutation(s): 2  Gene Names: qedH-II, PP_2679 EC: 1.1.2.8 (PDB Primary Data), 1.1.2 (UniProt)
UniProt
Find proteins for Q88JH0 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88JH0  Go to UniProtKB:  Q88JH0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PQQ (Subject of Investigation/LOI)	C [auth A]	PYRROLOQUINOLINE QUINONE C14 H6 N2 O8 MMXZSJMASHPLLR-UHFFFAOYSA-N
PR (Subject of Investigation/LOI)	D [auth A]	PRASEODYMIUM ION Pr WCWKKSOQLQEJTE-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.160 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.53	α = 90
b = 105.53	β = 90
c = 186.88	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Bange, G., Lepak, A., Elsayed, E.M.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary