3ISR | pdb_00003isr

The Crystal Structure of a Putative Cysteine Protease from Cytophaga hutchinsonii to 1.9A

• PDB DOI: https://doi.org/10.2210/pdb3ISR/pdb

• Classification: HYDROLASE
• Organism(s): Cytophaga hutchinsonii ATCC 33406
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-27 Released: 2009-09-08 
• Deposition Author(s): Stein, A.J., Bigelow, L., Trevino, D., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.220 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

The Crystal Structure of a Putative Cysteine Protease from Cytophaga hutchinsonii to 1.9A

Stein, A.J., Bigelow, L., Trevino, D., Buck, K., Joachimiak, A.

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.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 132.64 kDa 
• Atom Count: 9,509 
• Modeled Residue Count: 1,149 
• Deposited Residue Count: 1,172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transglutaminase-like enzymes, putative cysteine protease	A, B, C, D	293	Cytophaga hutchinsonii ATCC 33406	Mutation(s): 0  Gene Names: CHU_2601, CHU_261

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.220 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.716	α = 90
b = 115.24	β = 90
c = 131.262	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Stein, A.J., Bigelow, L., Trevino, D., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary