6L25 | pdb_00006l25

Deoxyribonuclease from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb6L25/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2019-10-02 Released: 2020-05-13 
• Deposition Author(s): Lee, K.-Y., Kim, D.-G., Lee, B.-J.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.236 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

A structural study of TatD from Staphylococcus aureus elucidates a putative DNA-binding mode of a Mg2+-dependent nuclease.

Lee, K.-Y., Cheon, S.-H., Kim, D.-G., Lee, S.J., Lee, B.-J.

(2020) IUCrJ 7: 509-521

• DOI: https://doi.org/10.1107/S2052252520003917

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 63.44 kDa 
• Atom Count: 4,283 
• Modeled Residue Count: 509 
• Deposited Residue Count: 546 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribonuclease YcfH	A, B	273	Staphylococcus aureus	Mutation(s): 0  Gene Names:  yabD, tatP, ycfH, ycfH_1, BN1321_120011, C7P97_09010, CSC83_12190, CSC87_02770, EP54_03105, EQ90_10980, ERS072840_02446, HMPREF3211_00370, M1K003_2676, NCTC10654_00570, NCTC10702_00886, NCTC13131_01111, NCTC5664_00191, NCTC7878_00052, RK64_02970, SAMEA1708674_03251 EC: 3.1.21
UniProt
Find proteins for W8U6D8 (Staphylococcus aureus) Explore W8U6D8  Go to UniProtKB:  W8U6D8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	E [auth A], F [auth A], I [auth B], J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NI (Subject of Investigation/LOI)	C [auth A], D [auth A], G [auth B], H [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-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: 1.85 Å
• R-Value Free:  0.236 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.627	α = 90
b = 77.832	β = 98.81
c = 77.378	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Lee, K.-Y., Kim, D.-G., Lee, B.-J.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2018R1A2A1A19018526
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2018R1A5A2024425
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2016R1C1B2014609
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2019R1H1A1102102

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary