3IVL | pdb_00003ivl

The Crystal Structure of the Inactive Peptidase Domain of a Putative Zinc Protease from Bordetella parapertussis to 2.2A

• PDB DOI: https://doi.org/10.2210/pdb3IVL/pdb

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


• Deposited: 2009-09-01 Released: 2009-09-08 
• Deposition Author(s): Stein, A.J., Wu, R., Keigher, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.258 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

The Crystal Structure of the Inactive Peptidase Domain of a Putative Zinc Protease from Bordetella parapertussis to 2.2A

Stein, A.J., Wu, R., Keigher, L., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.07 kDa 
• Atom Count: 2,826 
• Modeled Residue Count: 370 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative zinc protease	A, B	208	Bordetella parapertussis	Mutation(s): 0  Gene Names: BPP3483
UniProt
Find proteins for Q7W521 (Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)) Explore Q7W521  Go to UniProtKB:  Q7W521

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A], D [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-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: 2.20 Å
• R-Value Free:  0.258 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.173	α = 90
b = 108.173	β = 90
c = 113.995	γ = 120

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
HKL-3000	phasing
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., Wu, R., Keigher, L., 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, 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