3HVY

Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_348457.1) from Clostridium acetobutylicum at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3HVY/pdb

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


• Deposited: 2009-06-16 Released: 2009-06-30 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.187 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 

Literature

Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_348457.1) from Clostridium acetobutylicum at 2.00 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)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content

• Total Structure Weight: 195.7 kDa 
• Atom Count: 13,952 
• Modelled Residue Count: 1,681 
• Deposited Residue Count: 1,712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine beta-lyase family protein, YNBB B.subtilis ortholog	A, B, C, D	427	Clostridium acetobutylicum	Mutation(s): 0  Gene Names: CA_C1833, NP_348457.1
UniProt
Find proteins for Q97I22 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787)) Explore Q97I22  Go to UniProtKB:  Q97I22

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], R [auth C], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	E [auth A], K [auth B], Q [auth C], X [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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: 2.00 Å
• R-Value Free: 0.187 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M33HVY

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.83	α = 90
b = 186.62	β = 103.06
c = 93.71	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-30 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations