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- PDB-2cfm: ATP-DEPENDENT DNA LIGASE FROM PYROCOCCUS FURIOSUS -

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Basic information

Entry
Database: PDB / ID: 2cfm
TitleATP-DEPENDENT DNA LIGASE FROM PYROCOCCUS FURIOSUS
ComponentsTHERMOSTABLE DNA LIGASE
KeywordsLIGASE / PROTEIN-NUCLEOTIDE COMPLEX / CELL CYCLE / CELL DIVISION / DNA DAMAGE / DNA RECOMBINATION / DNA REPAIR / DNA REPLICATION / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


DNA ligation involved in DNA repair / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA biosynthetic process / DNA recombination / DNA replication / cell cycle / cell division / 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. / ATP-dependent DNA ligase AMP-binding site. ...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 MONOPHOSPHATE / DNA ligase
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsNishida, H. / Ishino, Y. / Morikawa, K.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The Closed Structure of an Archaeal DNA Ligase from Pyrococcus Furiosus.
Authors: Nishida, H. / Kiyonari, S. / Ishino, Y. / Morikawa, K.
History
DepositionFeb 22, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THERMOSTABLE DNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9913
Polymers64,6201
Non-polymers3722
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.866, 87.399, 62.648
Angle α, β, γ (deg.)90.00, 109.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein THERMOSTABLE DNA LIGASE / POLYDEOXYRIBONUCLEOTIDE SYNTHASE [ATP] / PFU DNA LIGASE


Mass: 64619.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: AMP IS BOUND IN THE POCKET NON-COVALENTLY / Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Plasmid: PET21D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P56709, DNA ligase (ATP)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.5 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ETHANOL, PH 8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 0.9797, 0.9791, 0.9787, 0.9587
DetectorType: RIGAKU RAXIS-IV / Detector: IMAGE PLATE / Date: Jun 21, 2004
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97911
30.97871
40.95871
ReflectionResolution: 1.8→30 Å / Num. obs: 56984 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.32 / % possible all: 98.5

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→30 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4051 7 %RANDOM
Rwork0.204 ---
obs0.204 56943 99.4 %-
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 24 450 4897
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.88 Å / % reflection Rfree: 7 % / % reflection obs: 98.5 %

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