6VBB | pdb_00006vbb

2.60 Angstrom Resolution Crystal Structure of Peptidase S41 from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb6VBB/pdb

• Classification: HYDROLASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-12-18 Released: 2019-12-25 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.237 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

2.60 Angstrom Resolution Crystal Structure of Peptidase S41 from Acinetobacter baumannii

Minasov, G., Wawrzak, Z., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Satchell, K.J.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: 85.11 kDa 
• Atom Count: 5,557 
• Modeled Residue Count: 686 
• Deposited Residue Count: 752 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase S41	A, B	376	Acinetobacter baumannii	Mutation(s): 0  Gene Names: BGC29_18875, CPI82_16465
UniProt
Find proteins for A0A1E3M7A1 (Acinetobacter baumannii) Explore A0A1E3M7A1  Go to UniProtKB:  A0A1E3M7A1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A], G [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
TMO	C [auth A]	trimethylamine oxide C3 H9 N O UYPYRKYUKCHHIB-UHFFFAOYSA-N
CL	F [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-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: 2.60 Å
• R-Value Free:  0.237 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.311	α = 90
b = 102.525	β = 116.28
c = 68.035	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Minasov, G., Wawrzak, Z., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2019-12-25
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary