8HDD

Complex structure of catalytic, small, and a partial electron transfer subunits from Burkholderia cepacia FAD glucose dehydrogenase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.278 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

Microgravity environment grown crystal structure information based engineering of direct electron transfer type glucose dehydrogenase

Okuda-Shimazaki, J., Yoshida, H., Lee, I., Kojima, K., Suzuki, N., Tsugawa, W., Yamada, M., Inaka, K., Tanaka, H., Sode, K.

(2022) Commun Biol 5: 1334


Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucose dehydrogenase539Burkholderia cepaciaMutation(s): 0 
Gene Names: gdhAlpha
EC: 1.1.5.9
UniProt
Find proteins for Q8GQE7 (Burkholderia cepacia)
Explore Q8GQE7 
Go to UniProtKB:  Q8GQE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GQE7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glucose dehydrogenase beta subunit482Burkholderia cepaciaMutation(s): 2 
UniProt
Find proteins for Q71JE9 (Burkholderia cepacia)
Explore Q71JE9 
Go to UniProtKB:  Q71JE9
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UniProt GroupQ71JE9
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Twin-arginine translocation pathway signal121Burkholderia cepaciaMutation(s): 0 
Gene Names: BMULJ_04411
UniProt
Find proteins for A0A0H3KLY3 (Burkholderia multivorans (strain ATCC 17616 / 249))
Explore A0A0H3KLY3 
Go to UniProtKB:  A0A0H3KLY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3KLY3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD
Download Ideal Coordinates CCD File 
D [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM
Download Ideal Coordinates CCD File 
F [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
F3S (Subject of Investigation/LOI)
Query on F3S
Download Ideal Coordinates CCD File 
E [auth A]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.278 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 204.015α = 90
b = 71.797β = 90
c = 114.221γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other privateJapanNA (sponsorship research)

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release