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- PDB-6l25: Deoxyribonuclease from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 6l25
TitleDeoxyribonuclease from Staphylococcus aureus
ComponentsDeoxyribonuclease YcfH
KeywordsMETAL BINDING PROTEIN / DNA binding protein / DNase / RNase / DNA repair system.
Function / homology
Function and homology information


DNA nuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / exonuclease activity / metal ion binding
Similarity search - Function
Uncharacterised hydrolase TatD-type / TatD deoxyribonuclease family signature 1. / TatD deoxyribonuclease family signature 3. / Deoxyribonuclease, TatD-related, conserved site / 3'-5' ssDNA/RNA exonuclease TatD-like / TatD related DNase / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / Deoxyribonuclease YcfH
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsLee, K.-Y. / Kim, D.-G. / Lee, B.-J.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2018R1A2A1A19018526 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2018R1A5A2024425 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2016R1C1B2014609 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2019R1H1A1102102 Korea, Republic Of
CitationJournal: Iucrj / Year: 2020
Title: A structural study of TatD from Staphylococcus aureus elucidates a putative DNA-binding mode of a Mg2+-dependent nuclease.
Authors: Lee, K.-Y. / Cheon, S.-H. / Kim, D.-G. / Lee, S.J. / Lee, B.-J.
History
DepositionOct 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyribonuclease YcfH
B: Deoxyribonuclease YcfH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,43610
Polymers62,8212
Non-polymers6158
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.627, 77.832, 77.378
Angle α, β, γ (deg.)90.000, 98.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Deoxyribonuclease YcfH / Hydrolase TatD / Hydrolase / TatD family / Metal-dependent DNase / Mg-dependent DNase / Putative ...Hydrolase TatD / Hydrolase / TatD family / Metal-dependent DNase / Mg-dependent DNase / Putative deoxyribonuclease YcfH / TatD family deoxyribonuclease


Mass: 31410.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: 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, ...Gene: 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
Production host: Escherichia coli K-12 (bacteria)
References: UniProt: W8U6D8, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.4 M sodium malonate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 47022 / % possible obs: 98.6 % / Redundancy: 9.6 % / CC1/2: 0.989 / Net I/σ(I): 41.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.8 % / Num. unique obs: 2125 / CC1/2: 0.872 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACTv3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.007 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 2398 5.1 %RANDOM
Rwork0.2105 ---
obs0.2118 44183 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.61 Å2 / Biso mean: 25.49 Å2 / Biso min: 12.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å2-0.21 Å2
2---1.15 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: final / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4088 0 24 171 4283
Biso mean--32.39 30.27 -
Num. residues----509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134192
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173885
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.6445677
X-RAY DIFFRACTIONr_angle_other_deg1.3811.5769039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5345507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50123.421228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16415714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3331522
X-RAY DIFFRACTIONr_chiral_restr0.0860.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024637
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02829
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 175 -
Rwork0.258 2917 -
all-3092 -
obs--87.97 %

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