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- PDB-2hix: ATP dependent DNA ligase from S. solfataricus bound to ATP -

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Basic information

Entry
Database: PDB / ID: 2hix
TitleATP dependent DNA ligase from S. solfataricus bound to ATP
ComponentsThermostable DNA ligase
KeywordsLIGASE / ATP-dependent DNA ligase / DNA replication
Function / homology
Function and homology information


DNA ligase (ATP) / DNA ligase (ATP) activity / DNA ligation / lagging strand elongation / DNA biosynthetic process / DNA recombination / cell division / DNA repair / DNA binding / ATP binding / metal ion binding
Similarity search - Function
DNA ligase, ATP-dependent, bacterial/archaeal / DNA ligase i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / : / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / DNA ligase/mRNA capping enzyme / ATP-dependent DNA ligase signature 2. ...DNA ligase, ATP-dependent, bacterial/archaeal / DNA ligase i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / : / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / DNA ligase/mRNA capping enzyme / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DNA ligase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsPascal, J.M. / Ellenberger, T.
CitationJournal: Mol.Cell / Year: 2006
Title: A Flexible Interface between DNA Ligase and PCNA Supports Conformational Switching and Efficient Ligation of DNA.
Authors: Pascal, J.M. / Tsodikov, O.V. / Hura, G.L. / Song, W. / Cotner, E.A. / Classen, S. / Tomkinson, A.E. / Tainer, J.A. / Ellenberger, T.
History
DepositionJun 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thermostable DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5062
Polymers69,9981
Non-polymers5071
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.324, 171.650, 78.686
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Thermostable DNA ligase / Polydeoxyribonucleotide synthase


Mass: 69998.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: lig / Production host: Escherichia coli (E. coli) / References: UniProt: Q980T8, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 6-8% PEG 3350, 50 mM sodium acetate pH 4.5, 30-80 mM sodium/potassium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.86→50 Å / Num. all: 18026 / Num. obs: 18026 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.077 / Χ2: 1.046 / Net I/σ(I): 14.4
Reflection shellResolution: 2.86→3 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.349 / Num. unique all: 1570 / Χ2: 0.866 / % possible all: 84.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.892 / SU B: 35.431 / SU ML: 0.316 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.431 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 916 5.1 %RANDOM
Rwork0.217 ---
all0.221 17962 --
obs0.217 17962 94.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.765 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å20 Å20 Å2
2---2.33 Å20 Å2
3---4.32 Å2
Refinement stepCycle: LAST / Resolution: 2.87→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4562 0 31 4 4597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224684
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9916322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6385577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93924.461204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.6915881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7891529
X-RAY DIFFRACTIONr_chiral_restr0.0860.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023442
X-RAY DIFFRACTIONr_nbd_refined0.2190.22062
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23217
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2152
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.26
X-RAY DIFFRACTIONr_mcbond_it0.4141.52943
X-RAY DIFFRACTIONr_mcangle_it0.74724628
X-RAY DIFFRACTIONr_scbond_it1.05431970
X-RAY DIFFRACTIONr_scangle_it1.7694.51693
LS refinement shellResolution: 2.87→2.938 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 41 -
Rwork0.316 835 -
obs-876 64.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.33280.10.36732.7368-0.57423.99160.152-0.2376-0.11380.69480.077-0.00690.34780.1798-0.2290.1063-0.0512-0.020.0127-0.0474-0.003929.373719.462348.742
24.10620.60620.97985.6917-2.00133.29590.08390.1512-0.154-0.12020.12510.42030.1618-0.026-0.209-0.2124-0.06030.0341-0.1479-0.0644-0.29818.522323.678415.3762
39.20111.48521.65924.1849-0.60535.4613-0.20490.18820.55260.3609-0.1305-0.929-0.38220.75020.3354-0.0345-0.026-0.02850.0696-0.00240.2528-10.162738.9458-2.3184
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 23021 - 250
32231 - 440251 - 460
43441 - 590461 - 610

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