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- PDB-6nhz: mycobacterial DNA ligase D complexed with ATP and Mg -

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Basic information

Entry
Database: PDB / ID: 6nhz
Titlemycobacterial DNA ligase D complexed with ATP and Mg
ComponentsATP-dependent DNA ligase
KeywordsLIGASE / DNA ligase
Function / homology
Function and homology information


DNA ligase (ATP) / DNA ligase (ATP) activity / DNA recombination / DNA repair / ATP binding
Similarity search - Function
DNA ligase D, ligase domain / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ATP-dependent DNA ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsShuman, S. / Unciuleac, M. / Goldgur, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30-CA008748 United States
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates.
Authors: Unciuleac, M.C. / Goldgur, Y. / Shuman, S.
History
DepositionDec 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7844
Polymers34,2291
Non-polymers5563
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-14 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.618, 51.630, 72.874
Angle α, β, γ (deg.)90.00, 99.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP-dependent DNA ligase


Mass: 34228.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ERS027656_00724
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0T9BTX3, DNA ligase (ATP)
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20 mM MgCl2 0.1 M NH4F 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 25765 / % possible obs: 94.9 % / Redundancy: 3.2 % / CC1/2: 0.99 / Rpim(I) all: 0.04 / Net I/σ(I): 16.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.7 / CC1/2: 0.849 / Rpim(I) all: 0.236 / % possible all: 85.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.8→29.492 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.63
RfactorNum. reflection% reflection
Rfree0.2439 2000 7.77 %
Rwork0.2061 --
obs0.209 25742 94.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2365 0 33 234 2632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062453
X-RAY DIFFRACTIONf_angle_d0.9813330
X-RAY DIFFRACTIONf_dihedral_angle_d8.2091451
X-RAY DIFFRACTIONf_chiral_restr0.056350
X-RAY DIFFRACTIONf_plane_restr0.005433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7982-1.84320.37141260.32111496X-RAY DIFFRACTION85
1.8432-1.8930.33361290.28621525X-RAY DIFFRACTION85
1.893-1.94870.30761300.24681560X-RAY DIFFRACTION90
1.9487-2.01160.25991470.23381731X-RAY DIFFRACTION95
2.0116-2.08350.28741460.23081742X-RAY DIFFRACTION98
2.0835-2.16690.27661470.22361734X-RAY DIFFRACTION98
2.1669-2.26550.27031460.22981740X-RAY DIFFRACTION98
2.2655-2.38480.26941450.21691726X-RAY DIFFRACTION96
2.3848-2.53420.27411440.22141705X-RAY DIFFRACTION97
2.5342-2.72970.24221410.22121672X-RAY DIFFRACTION93
2.7297-3.00420.23761480.20541764X-RAY DIFFRACTION98
3.0042-3.43830.24721500.20211779X-RAY DIFFRACTION99
3.4383-4.32970.21741520.16981795X-RAY DIFFRACTION99
4.3297-29.49550.19361490.18061773X-RAY DIFFRACTION96

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