3T9G

The crystal structure of family 3 pectate lyase from Caldicellulosiruptor bescii

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

A 1.5 A resolution X-ray structure of the catalytic module of Caldicellulosiruptor bescii family 3 pectate lyase.

Alahuhta, M., Chandrayan, P., Kataeva, I., Adams, M.W., Himmel, M.E., Lunin, V.V.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1498-1500

  • DOI: https://doi.org/10.1107/S1744309111038449
  • Primary Citation of Related Structures:  
    3T9G

  • PubMed Abstract: 

    • A 1.5 Å resolution X-ray structure of the catalytic module of Caldicellulosiruptor bescii family 3 pectate lyase is reported (PDB entry 3t9g). The resulting structure was refined to an R factor of 0.143 and an R(free) of 0.178. Structural analysis shows that this new structure is very similar to the previously solved structure of a family 3 pectate lyase from Bacillus sp ...

    A 1.5 Å resolution X-ray structure of the catalytic module of Caldicellulosiruptor bescii family 3 pectate lyase is reported (PDB entry 3t9g). The resulting structure was refined to an R factor of 0.143 and an R(free) of 0.178. Structural analysis shows that this new structure is very similar to the previously solved structure of a family 3 pectate lyase from Bacillus sp. strain KSM-P15 (PDB entry 1ee6), with a root-mean-square deviation of 0.93 Å and a sequence identity of 53%. This structural similarity is significant considering that C. bescii is a hyperthermophile and Bacillus sp. is a mesophile.

    Organizational Affiliation: 

    BioSciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pectate lyase
A, B
196Caldicellulosiruptor besciiMutation(s): 0 
Gene Names: Athe_1854, Cbes_1854
EC: 4.2.2.2
UniProt
Find proteins for B9MKT4 (Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / KCTC 15123 / Z-1320))
Explore B9MKT4 
Go to UniProtKB:  B9MKT4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9MKT4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD
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F [auth A],
G [auth A],
N [auth B],
O [auth B]		(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
MRD
Query on MRD
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D [auth A],
E [auth A],
M [auth B],
P [auth B]		(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N		 Ligand Interaction
PO4
Query on PO4
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AA [auth B],
Z [auth B]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
GOL
Query on GOL
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I [auth A],
J [auth A],
V [auth B],
W [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
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Q [auth B],
R [auth B]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
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X [auth B],
Y [auth B]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
CA
Query on CA
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C [auth A],
K [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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L [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
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H [auth A],
S [auth B],
T [auth B],
U [auth B]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.514α = 90
b = 146.685β = 90
c = 162.159γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
MOLREPphasing
REFMACrefinement
SAINTdata reduction
PROTEUM PLUSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description