3WY6 | pdb_00003wy6

Structure of hyperthermophilic family 12 endocellulase (E197A) from Pyrococcus furiosus in complex with laminaribiose

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.178 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.126 (Depositor), 0.126 (DCC) 
  • R-Value Observed: 
    0.128 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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

Literature

Structure of hyperthermophilic family 12 endocellulase (E197A) from Pyrococcus furiosus in complex with laminaribiose

Kataoka, M., Ishikawa, K.

To be published.

Macromolecule Content 

  • Total Structure Weight: 38.13 kDa 
  • Atom Count: 2,623 
  • 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): 1 
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-(1-3)-beta-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan: G36535HU
GlyCosmos: G36535HU

Small Molecules

Ligands 4 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]		2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
BGC

Query on BGC


Download:Ideal Coordinates CCD File
I [auth A]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
GOL

Query on GOL


Download:Ideal Coordinates CCD File
J [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [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

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.178 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.126 (Depositor), 0.126 (DCC) 
  • R-Value Observed: 0.128 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.03α = 90
b = 118.865β = 90
c = 46.873γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-03-20
    Changes: Data collection, Database references, Structure summary