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)

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)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

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

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| 3D Structure

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... 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W8U6D8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], I [auth B], J [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]
NI (Subject of Investigation/LOI) Query on NI Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], G [auth B], H [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Lee, K.-Y.

Kim, D.-G.

Lee, B.-J.

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 (Full details and data files)

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

6L25 | pdb_00006l25

Deoxyribonuclease from Staphylococcus aureus

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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