3ZSC | pdb_00003zsc

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

• PDB DOI: https://doi.org/10.2210/pdb3ZSC/pdb

• Classification: LYASE
• Organism(s): Thermotoga maritima
• Expression System: Bacillus licheniformis
• Mutation(s): Yes 


• Deposited: 2011-06-24 Released: 2012-07-11 
• Deposition Author(s): McDonough, M.A., Thymark, M., Frisner, H., Hotchkiss, A., Sonksen, C., Bjornvad, M., Johansen, K.S., Larsen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.237 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.179 (Depositor) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 38.57 kDa 
• Atom Count: 2,794 
• Modeled Residue Count: 329 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PECTATE TRISACCHARIDE-LYASE	A	340	Thermotoga maritima	Mutation(s): 3  EC: 4.2.2.22
UniProt
Find proteins for Q9WYR4 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYR4  Go to UniProtKB:  Q9WYR4

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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
Glycosylation Resources
GlyTouCan: G68931OA GlyCosmos: G68931OA

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.237 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.179 (Depositor) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.602	α = 90
b = 80.602	β = 90
c = 148.819	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): McDonough, M.A., Thymark, M., Frisner, H., Hotchkiss, A., Sonksen, C., Bjornvad, M., Johansen, K.S., Larsen, S.

Revision History  

• 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
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary