3IFE | pdb_00003ife

1.55 Angstrom Resolution Crystal Structure of Peptidase T (pepT-1) from Bacillus anthracis str. 'Ames Ancestor'.

• PDB DOI: https://doi.org/10.2210/pdb3IFE/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus anthracis str. 'Ames Ancestor
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-24 Released: 2009-08-04 
• Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.172 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

1.55 Angstrom Resolution Crystal Structure of Peptidase T (pepT-1) from Bacillus anthracis str. 'Ames Ancestor'.

Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 49.73 kDa 
• Atom Count: 4,262 
• Modeled Residue Count: 416 
• Deposited Residue Count: 434 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase T	A	434	Bacillus anthracis str. 'Ames Ancestor	Mutation(s): 0  Gene Names: BAS3588, BA_3872, GBAA_3872, pepT, pepT-1 EC: 3.4.11.4
UniProt
Find proteins for Q81WU4 (Bacillus anthracis) Explore Q81WU4  Go to UniProtKB:  Q81WU4

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B, C	2		N/A
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	B, C	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.172 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33ife

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.216	α = 90
b = 142.739	β = 90
c = 40.993	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
CRANK	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-04 
Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary