3WQ1 | pdb_00003wq1

Structure of hyperthermophilic family 12 endocellulase from Pyrococcus furiosus in complex with cello-oligosaccharide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.139 (Depositor), 0.142 (DCC) 
  • R-Value Work: 
    0.112 (Depositor) 
  • R-Value Observed: 
    0.113 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history. 

Literature

Structure of hyperthermophilic family 12 endocellulase from Pyrococcus furiosus in complex with cello-oligosaccharide

Kataoka, M., Ishikawa, K.

To be published.

Macromolecule Content 

  • Total Structure Weight: 38.08 kDa 
  • Atom Count: 2,760 
  • Modeled Residue Count: 270 
  • Deposited Residue Count: 319 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endoglucanase A319Pyrococcus furiosusMutation(s): 0 
Gene Names: eglA
EC: 3.2.1.4
UniProt
Find proteins for Q9V2T0 (Pyrococcus furiosus)
Explore Q9V2T0 
Go to UniProtKB:  Q9V2T0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V2T0
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose
B
4N/A
Glycosylation Resources
GlyTouCan: G75242TK
GlyCosmos: G75242TK
GlyGen: G75242TK

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NHE

Query on NHE


Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]		2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
GOL

Query on GOL


Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
L [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.139 (Depositor), 0.142 (DCC) 
  • R-Value Work:  0.112 (Depositor) 
  • R-Value Observed: 0.113 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.14α = 90
b = 118.42β = 90
c = 46.79γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-03-20
    Changes: Data collection, Database references, Structure summary