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- PDB-1fvi: CRYSTAL STRUCTURE OF CHLORELLA VIRUS DNA LIGASE-ADENYLATE -

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Basic information

Entry
Database: PDB / ID: 1fvi
TitleCRYSTAL STRUCTURE OF CHLORELLA VIRUS DNA LIGASE-ADENYLATE
ComponentsCHLORELLA VIRUS DNA LIGASE-ADENYLATE
KeywordsLIGASE / adenylated DNA ligase
Function / homology
Function and homology information


DNA ligation involved in DNA repair / DNA ligase (ATP) activity / DNA recombination / DNA repair / ATP binding
Similarity search - Function
DNA ligase, OB-like domain / DNA ligase OB-like domain / Dna Ligase; domain 1 - #70 / ATP-dependent DNA ligase signature 2. / DNA ligase/mRNA capping enzyme / DNA ligase, ATP-dependent, conserved site / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins ...DNA ligase, OB-like domain / DNA ligase OB-like domain / Dna Ligase; domain 1 - #70 / ATP-dependent DNA ligase signature 2. / DNA ligase/mRNA capping enzyme / DNA ligase, ATP-dependent, conserved site / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DNA ligase / DNA ligase
Similarity search - Component
Biological speciesChlorella virus
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsOdell, M. / Sriskanda, V. / Shuman, S. / Nikolov, D.B.
CitationJournal: Mol.Cell / Year: 2000
Title: Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining.
Authors: Odell, M. / Sriskanda, V. / Shuman, S. / Nikolov, D.B.
History
DepositionSep 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: CHLORELLA VIRUS DNA LIGASE-ADENYLATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5673
Polymers34,1241
Non-polymers4432
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.17, 58.44, 101.79
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CHLORELLA VIRUS DNA LIGASE-ADENYLATE


Mass: 34124.195 Da / Num. of mol.: 1 / Mutation: D29A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorella virus / Genus: Chlorovirus / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O41026, UniProt: A7RCB1*PLUS, Ligases; Forming phosphoric-ester bonds
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl1drop
25 mMdithiothreitol1drop
318 mg/mlprotein1drop
4100 mM1dropNaCl
550 mMTris-HCl1reservoir
65 mMdithiothreitol1reservoir
7100 mM1reservoirNaCl
81.8-2.0 Mammonium sulfate1reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 98.6 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.045

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Processing

Software
NameClassification
MLPHAREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→6 Å / σ(F): 1.5 / σ(I): 1.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.27 1125 random
Rwork0.19 --
all-18470 -
obs-18130 -
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 27 280 2430
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.548
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / σ(F): 1.5 / Rfactor obs: 0.185 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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