3BM3 | pdb_00003bm3

Restriction endonuclease PspGI-substrate DNA complex

• PDB DOI: https://doi.org/10.2210/pdb3BM3/pdb
• NAKB: 3BM3

• Classification: HYDROLASE/DNA
• Organism(s): Pyrococcus sp. GI-H
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-12-12 Released: 2008-09-16 
• Deposition Author(s): Szczepanowski, R.H., Carpenter, M., Czapinska, H., Tamulaitis, G., Siksnys, V., Bhagwat, A., Bochtler, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.192 (Depositor) 
• R-Value Work: 
  0.170 (Depositor) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

A direct crystallographic demonstration that Type II restriction endonuclease PspGI flips nucleotides

Szczepanowski, R.H., Carpenter, M., Czapinska, H., Tamulaitis, G., Siksnys, V., Bhagwat, A., Bochtler, M.

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: 71.33 kDa 
• Atom Count: 5,301 
• Modeled Residue Count: 539 
• Deposited Residue Count: 566 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PspGI restriction endonuclease	C [auth A], D [auth B]	272	Pyrococcus sp. GI-H	Mutation(s): 2
UniProt
Find proteins for O93646 (Pyrococcus sp. GI-H) Explore O93646  Go to UniProtKB:  O93646

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*TP*CP*CP*AP*GP*GP*TP*AP*C)-3')	A [auth C]	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*TP*AP*CP*CP*TP*GP*GP*AP*T)-3')	B [auth D]	11	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	E [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.192 (Depositor) 
• R-Value Work:  0.170 (Depositor) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.884	α = 90
b = 96.06	β = 90
c = 127.069	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
SHELXE	model building
DM	model building
ARP/wARP	model building
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-16 
Deposition Author(s): Szczepanowski, R.H., Carpenter, M., Czapinska, H., Tamulaitis, G., Siksnys, V., Bhagwat, A., Bochtler, M.

Revision History  

• Version 1.0: 2008-09-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description
• Version 1.3: 2021-10-20
  Changes: Advisory, Database references, Derived calculations
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary