2DP6 | pdb_00002dp6

Crystal structure of uracil-DNA glycosylase in complex with AP:C containing DNA

• PDB DOI: https://doi.org/10.2210/pdb2DP6/pdb
• NAKB: 2DP6

• Classification: HYDROLASE/DNA
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-05-07 Released: 2007-05-22 
• Deposition Author(s): Kosaka, H., Nakagawa, N., Masui, R., Kuramitsu, S., Hoseki, J., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.217 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.199 (DCC) 

Starting Model: experimental

Literature

Structure of Family 5 Uracil-DNA Glycosylase Bound to DNA Reveals Insights into the Mechanism for Substrate Recognition and Catalysis

Kosaka, H., Nakagawa, N., Masui, R., Kuramitsu, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.84 kDa 
• Atom Count: 2,537 
• Modeled Residue Count: 248 
• Deposited Residue Count: 248 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
uracil-DNA glycosylase	C [auth A]	219	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: ttUDGB EC: 3.2.2
UniProt
Find proteins for Q5SJ65 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ65  Go to UniProtKB:  Q5SJ65

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*TP*GP*TP*TP*GP*CP*(D1P)P*TP*TP*AP*GP*TP*CP*C)-3'	A [auth C]	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*AP*CP*TP*AP*AP*CP*GP*CP*AP*AP*CP*A)-3'	B [auth D]	14	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	E [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
2HP	D, F [auth A]	DIHYDROGENPHOSPHATE ION H2 O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-M
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EOH	I [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.217 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.199 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.868	α = 90
b = 148.754	β = 90
c = 93.086	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
HKL-2000	data reduction
MLPHARE	phasing
CNS	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-22 
Deposition Author(s): Kosaka, H., Nakagawa, N., Masui, R., Kuramitsu, S., Hoseki, J., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-05-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description