2F6K | pdb_00002f6k

Crystal Structure of Amidohydrorolase II; Northeast Structural Genomics Target LpR24

• PDB DOI: https://doi.org/10.2210/pdb2F6K/pdb

• Classification: LYASE
• Organism(s): Lactiplantibacillus plantarum WCFS1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-11-29 Released: 2006-01-10 
• Deposition Author(s): Das, K., Xiao, R., Acton, T., Ma, L., Arnold, E., Montelione, G.T., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.225 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Crystal Structure of ACMDS from Lactobacillus plantarum

Das, K., Xiao, R., Acton, T., Ma, L., Arnold, E., Montelione, G.T.

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.

Macromolecule Content 

• Total Structure Weight: 69.82 kDa 
• Atom Count: 5,119 
• Modeled Residue Count: 612 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
metal-dependent hydrolase	A, B	307	Lactiplantibacillus plantarum WCFS1	Mutation(s): 7  EC: 4.1.1.45 (PDB Primary Data), 4.1.1.52 (UniProt)
UniProt
Find proteins for F9US96 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9US96  Go to UniProtKB:  F9US96

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A], D [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.225 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.62	α = 90
b = 82.62	β = 90
c = 240.815	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-10 
Deposition Author(s): Das, K., Xiao, R., Acton, T., Ma, L., Arnold, E., Montelione, G.T., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2006-01-10
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary