3LHL | pdb_00003lhl

Crystal structure of a putative agmatinase from Clostridium difficile

• PDB DOI: https://doi.org/10.2210/pdb3LHL/pdb

• Classification: HYDROLASE
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-22 Released: 2010-02-23 
• Deposition Author(s): Palani, K., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.238 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Crystal structure of a putative agmatinase from Clostridium difficile

Palani, K., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.43 kDa 
• Atom Count: 2,393 
• Modeled Residue Count: 276 
• Deposited Residue Count: 287 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative agmatinase	A	287	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD0891, speB EC: 3.5.3.11
UniProt
Find proteins for Q18A84 (Clostridioides difficile (strain 630)) Explore Q18A84  Go to UniProtKB:  Q18A84

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	H [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4	F [auth A], G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN	B [auth A], C [auth A], D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.238 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.35	α = 90
b = 77.35	β = 90
c = 166.118	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Palani, K., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Structure summary