3GWP

Crystal structure of carbon-sulfur lyase involved in aluminum resistance (YP_878183.1) from CLOSTRIDIUM NOVYI NT at 2.90 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3GWP/pdb

• Classification: LYASE
• Organism(s): Clostridium novyi NT
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-01 Released: 2009-04-14 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.271 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Starting Model: experimental

Literature

Crystal structure of carbon-sulfur lyase involved in aluminum resistance (YP_878183.1) from CLOSTRIDIUM NOVYI NT at 2.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 192.05 kDa 
• Atom Count: 12,910 
• Modelled Residue Count: 1,696 
• Deposited Residue Count: 1,708 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
carbon-sulfur lyase involved in aluminum resistance	A, B, C, D	427	Clostridium novyi NT	Mutation(s): 0  Gene Names: NT01CX_2110, YP_878183.1
UniProt
Find proteins for A0Q0N1 (Clostridium novyi (strain NT)) Explore A0Q0N1  Go to UniProtKB:  A0Q0N1

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.271 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M33GWP

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.74	α = 90
b = 108.948	β = 90
c = 207.642	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
PHASER	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-14 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-04-14
  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: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references
• Version 1.5: 2023-09-20
  Changes: Data collection, Refinement description
• Version 1.6: 2023-11-22
  Changes: Data collection