3A9H

Crystal Structure of PQQ-dependent sugar dehydrogenase holo-form

• PDB DOI: https://doi.org/10.2210/pdb3A9H/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pyrobaculum aerophilum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-26 Released: 2010-09-08 
• Deposition Author(s): Sakuraba, H., Yokono, K., Yoneda, K., Ohshima, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.231 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 39.43 kDa 
• Atom Count: 2,742 
• Modelled Residue Count: 338 
• Deposited Residue Count: 354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	354	Pyrobaculum aerophilum	Mutation(s): 0  EC: 1.1.5.2
UniProt
Find proteins for Q8ZUN8 (Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2)) Explore Q8ZUN8  Go to UniProtKB:  Q8ZUN8

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	B, C	2		N/A
Glycosylation Resources
GlyTouCan:  G92130SN GlyCosmos:  G92130SN

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PQQ	E [auth A]	PYRROLOQUINOLINE QUINONE C14 H6 N2 O8 MMXZSJMASHPLLR-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006	B, C	trehalose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.231 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.344	α = 90
b = 177.344	β = 90
c = 89.743	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Sakuraba, H., Yokono, K., Yoneda, K., Ohshima, T.

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary