3ZSC

Catalytic function and substrate recognition of the pectate lyase from Thermotoga maritima


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Catalytic Function and Substrate Recognition of the Pectate Lyase from Thermotoga Maritima

McDonough, M.A.Thymark, M.Frisner, H.Hotchkiss, A.Sonksen, C.Bjornvad, M.Johansen, K.S.Larsen, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PECTATE TRISACCHARIDE-LYASE A340Thermotoga maritimaMutation(s): 3 
EC: 4.2.2.22
Find proteins for Q9WYR4 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Explore Q9WYR4 
Go to UniProtKB:  Q9WYR4
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
4-deoxy-beta-L-threo-hex-4-enopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid
B
3 N/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.602α = 90
b = 80.602β = 90
c = 148.819γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
EPMRphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary