5F5X | pdb_00005f5x

Crystal structure of S116A Ba3275 with AMP bound

• PDB DOI: https://doi.org/10.2210/pdb5F5X/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus cereus ATCC 10987
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2015-12-04 Released: 2015-12-30 
• Deposition Author(s): Nocek, B., Severinov, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

Crystal structure of Ba3275-AMP complex from Bacillus cereus ATCC 10987

Nocek, B., Severinov, K., Anderson, W.F., 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.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 80.81 kDa 
• Atom Count: 5,854 
• Modeled Residue Count: 688 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MccC family protein Ba3275	A, B	346	Bacillus cereus ATCC 10987	Mutation(s): 2  Gene Names: BCE_3281
UniProt
Find proteins for Q734X3 (Bacillus cereus (strain ATCC 10987 / NRS 248)) Explore Q734X3  Go to UniProtKB:  Q734X3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A], D [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-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: 2.01 Å
• R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.116	α = 90
b = 117.728	β = 95.27
c = 54.852	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2015-12-30
  Type: Initial release
  
• Version 1.1: 2016-01-20
  Changes: Structure summary
• Version 1.2: 2017-02-08
  Changes: Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary