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- PDB-3gde: The closed conformation of ATP-dependent DNA ligase from Archaeog... -

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Basic information

Entry
Database: PDB / ID: 3gde
TitleThe closed conformation of ATP-dependent DNA ligase from Archaeoglobus fulgidus
ComponentsDNA ligase
KeywordsLIGASE / ATP-dependent DNA ligase / DNA-binding domain / adenylation domain / OB-fold domain / ATP-binding / 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
PHOSPHATE ION / DNA ligase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKim, D.J. / Kim, H.-W. / Kim, O. / Kim, H.S. / Lee, S.J. / Suh, S.W.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: ATP-dependent DNA ligase from Archaeoglobus fulgidus displays a tightly closed conformation
Authors: Kim, D.J. / Kim, O. / Kim, H.-W. / Kim, H.S. / Lee, S.J. / Suh, S.W.
History
DepositionFeb 24, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3115
Polymers63,9311
Non-polymers3804
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.355, 94.355, 197.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DNA ligase / ATP-dependent DNA ligase / Polydeoxyribonucleotide synthase [ATP]


Mass: 63931.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF0623 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: O29632, DNA ligase (ATP)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 3.44 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100mM Tris-HCl, pH9.0, 0.4M sodium dihydrogen phosphate, 1.2M dipotassium hydrogen phosphate, 10mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 40500 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.089 / Net I/σ(I): 36
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 5.1 / Rsym value: 0.44 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CFM

2cfm


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.916 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.278 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 4007 9.9 %RANDOM
Rwork0.215 ---
obs0.221 36294 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 216.28 Å2 / Biso mean: 37.035 Å2 / Biso min: 2.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20 Å2
2--1.62 Å20 Å2
3----3.25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 20 458 4901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224513
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9886073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2465549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16623.382204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.9215874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3561542
X-RAY DIFFRACTIONr_chiral_restr0.0980.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023309
X-RAY DIFFRACTIONr_nbd_refined0.1980.22322
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23087
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2420
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.228
X-RAY DIFFRACTIONr_mcbond_it0.6831.52823
X-RAY DIFFRACTIONr_mcangle_it1.18924418
X-RAY DIFFRACTIONr_scbond_it1.62231896
X-RAY DIFFRACTIONr_scangle_it2.7654.51655
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 255 -
Rwork0.25 2625 -
all-2880 -
obs--99.79 %

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