1G2I | pdb_00001g2i

CRYSTAL STRUCTURE OF A NOVEL INTRACELLULAR PROTEASE FROM PYROCOCCUS HORIKOSHII AT 2 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1G2I/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-10-19 Released: 2000-11-08 
• Deposition Author(s): Du, X., Choi, I.-G., Kim, R., Jancarik, J., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.200 (Depositor) 
• R-Value Work: 
  0.184 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal structure of an intracellular protease from Pyrococcus horikoshii at 2-A resolution.

Du, X., Choi, I.G., Kim, R., Wang, W., Jancarik, J., Yokota, H., Kim, S.-H.

(2000) Proc Natl Acad Sci U S A 97: 14079-14084

• PubMed: 11114201 
• DOI: https://doi.org/10.1073/pnas.260503597
• Primary Citation Related Structures: 
  1G2I


• PubMed Abstract: 
  

  The intracellular protease from Pyrococcus horikoshii (PH1704) and PfpI from Pyrococcus furiosus are members of a class of intracellular proteases that have no sequence homology to any other known protease family. We report the crystal structure of PH1704 at 2.0-A resolution. The protease is tentatively identified as a cysteine protease based on the presence of cysteine (residue 100) in a nucleophile elbow motif. In the crystal, PH1704 forms a hexameric ring structure, and the active sites are formed at the interfaces between three pairs of monomers.

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Organizational Affiliation: 
• Department of Chemistry, University of California, Berkeley, CA 94720, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.61 kDa 
• Atom Count: 4,224 
• Modeled Residue Count: 498 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASE I	A, B, C	166	Pyrococcus horikoshii	Mutation(s): 4  Gene Names: PH1704 EC: 3.2 (PDB Primary Data), 3.4.22 (UniProt), 3.5.1.124 (UniProt)
UniProt
Find proteins for O59413 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59413  Go to UniProtKB:  O59413

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.200 (Depositor) 
• R-Value Work:  0.184 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.7	α = 90
b = 124.7	β = 90
c = 129	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-11-08 
Deposition Author(s): Du, X., Choi, I.-G., Kim, R., Jancarik, J., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

Revision History  

• Version 1.0: 2000-11-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-02-08
  Changes: Structure summary
• Version 1.4: 2018-01-24
  Changes: Structure summary
• Version 1.5: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary