3BM3

Restriction endonuclease PspGI-substrate DNA complex


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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.

Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PspGI restriction endonucleaseC [auth A],
D [auth B]
272Pyrococcus sp. GI-HMutation(s): 2 
UniProt
Find proteins for O93646 (Pyrococcus sp. GI-H)
Explore O93646 
Go to UniProtKB:  O93646
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO93646
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*AP*TP*CP*CP*AP*GP*GP*TP*AP*C)-3')A [auth C]11N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*GP*TP*AP*CP*CP*TP*GP*GP*AP*T)-3')B [auth D]11N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
E [auth B]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
C [auth A],
D [auth B]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.884α = 90
b = 96.06β = 90
c = 127.069γ = 90
Software Package:
Software NamePurpose
SHELXDphasing
SHELXEmodel building
DMmodel building
ARP/wARPmodel building
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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