5FD8 | pdb_00005fd8

Crystal Structure of MccF-like Protein (BA_5613) in complex with ASA (alanyl sulfamoyl adenylates)

• PDB DOI: https://doi.org/10.2210/pdb5FD8/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus anthracis str. Ames
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2015-12-15 Released: 2015-12-30 
• Deposition Author(s): Nocek, B., Severinov, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Crystal Structure of MccF-like Protein (BA_5613) in complex with ASA ( (alanyl sulfamoyl adenylates)

Nocek, B., Severinov, K., 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: 75.5 kDa 
• Atom Count: 5,493 
• Modeled Residue Count: 660 
• Deposited Residue Count: 662 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LD-carboxypeptidase family protein	A, B	331	Bacillus anthracis str. Ames	Mutation(s): 0  Gene Names: yocD
UniProt
Find proteins for A0A6L8PVW7 (Bacillus anthracis) Explore A0A6L8PVW7  Go to UniProtKB:  A0A6L8PVW7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A5A	C [auth A], D [auth B]	'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE C13 H19 N7 O7 S CWWYMWDIYBJVLP-YTMOPEAISA-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: 2.05 Å
• R-Value Free:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35fd8

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.777	α = 90
b = 83.683	β = 90
c = 130.845	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SBC-Collect	data collection
HKL-3000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-30 
Deposition Author(s): Nocek, B., Severinov, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2015-12-30
  Type: Initial release
  
• Version 1.1: 2016-01-13
  Changes: Other
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Structure summary