6ZCW | pdb_00006zcw

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

PDB DOI: https://doi.org/10.2210/pdb6ZCW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida KT2440
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.172 (Depositor), 0.174 (DCC)
R-Value Work:
0.156 (Depositor), 0.159 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

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

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

(2020) ACS Catal 10: 7836-7842

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

Macromolecule Content

Total Structure Weight: 63.56 kDa
Atom Count: 5,042
Modeled Residue Count: 562
Deposited Residue Count: 575
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Quinoprotein ethanol dehydrogenase	A	575	Pseudomonas putida KT2440	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q88JH0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PQQ (Subject of Investigation/LOI) Query on PQQ Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PYRROLOQUINOLINE QUINONE C₁₄ H₆ N₂ O₈ MMXZSJMASHPLLR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PR Query on PR Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PRASEODYMIUM ION Pr WCWKKSOQLQEJTE-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.172 (Depositor), 0.174 (DCC)
R-Value Work: 0.156 (Depositor), 0.159 (DCC)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.28	α = 90
b = 105.28	β = 90
c = 187.13	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-15

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2020-07-15
Type: Initial release
Version 1.1: 2021-08-11
Changes: Advisory, Database references
Version 1.2: 2024-01-24
Changes: Data collection, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.