3GLV | pdb_00003glv

Crystal structure of the lipopolysaccharide core biosynthesis protein from Thermoplasma volcanium GSS1

• PDB DOI: https://doi.org/10.2210/pdb3GLV/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Thermoplasma volcanium GSS1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-12 Released: 2009-05-12 
• Deposition Author(s): Zhang, R., Sather, A., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

The crystal structure of the lipopolysaccharide core biosynthesis protein from Thermoplasma volcanium GSS1

Zhang, R., Sather, A., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 32.72 kDa 
• Atom Count: 2,117 
• Modelled Residue Count: 244 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipopolysaccharide core biosynthesis protein	A, B	143	Thermoplasma volcanium GSS1	Mutation(s): 0  Gene Names: GI:14325477, TV1239, TVG1279046 EC: 2.7.7.2
UniProt
Find proteins for Q979C2 (Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1)) Explore Q979C2  Go to UniProtKB:  Q979C2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	D [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.391	α = 90
b = 67.187	β = 90
c = 99.032	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-12 
Deposition Author(s): Zhang, R., Sather, A., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations