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- PDB-1dgs: CRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS -

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Basic information

Entry
Database: PDB / ID: 1dgs
TitleCRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS
ComponentsDNA LIGASE
KeywordsLIGASE / AMP COMPLEX / NAD+-DEPENDENT
Function / homology
Function and homology information


DNA ligase (NAD+) / DNA ligase (NAD+) activity / base-excision repair, DNA ligation / DNA replication / DNA binding / metal ion binding / cytosol
Similarity search - Function
Dna Ligase; domain 1 - #70 / Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation ...Dna Ligase; domain 1 - #70 / Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation / NAD-dependent DNA ligase, N-terminal / NAD-dependent DNA ligase adenylation domain / NAD-dependent DNA ligase OB-fold domain / Ligase N family / DisA/LigA, helix-hairpin-helix motif / Helix-hairpin-helix motif / DNA ligase/mRNA capping enzyme / Helix hairpin bin / RuvA domain 2-like / Helix-hairpin-helix domain / BRCA1 C Terminus (BRCT) domain / D-amino Acid Aminotransferase; Chain A, domain 1 / breast cancer carboxy-terminal domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding proteins / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / 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 speciesThermus filiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsLee, J.Y. / Chang, C. / Song, H.K. / Kwon, S.T. / Suh, S.W.
CitationJournal: EMBO J. / Year: 2000
Title: Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.
Authors: Lee, J.Y. / Chang, C. / Song, H.K. / Moon, J. / Yang, J.K. / Kim, H.K. / Kwon, S.T. / Suh, S.W.
History
DepositionNov 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA LIGASE
B: DNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,8216
Polymers151,9962
Non-polymers8254
Water4,360242
1
A: DNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4113
Polymers75,9981
Non-polymers4132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4113
Polymers75,9981
Non-polymers4132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.210, 117.330, 97.480
Angle α, β, γ (deg.)90.00, 115.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA LIGASE


Mass: 75997.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: AMP IS BONDED TO LYS116 / Source: (natural) Thermus filiformis (bacteria) / References: UniProt: Q9ZHI0, DNA ligase (NAD+)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 3.04 Å3/Da / Density % sol: 59.52 %
Description: INVERSE BEAM GEOMETRY AT THREE WAVELENTHS METHOD USED TO DETERMINE THE STRUCTURE: MAD
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6 / Details: pH 5.6, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMsodium citrate1reservoir
25 %MPEG50001reservoir
35 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9400, 0.9784, 0.9788
DetectorType: BRANDEIS / Detector: CCD / Date: Mar 1, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.941
20.97841
30.97881
ReflectionResolution: 2.9→30 Å / Num. obs: 40641 / % possible obs: 97.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.8
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 4 / % possible all: 79.2
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 215788 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 79.2 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.9→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 114414.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.298 3616 10 %RANDOM
Rwork0.228 ---
obs-36060 89.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 13.4 Å2 / ksol: 0.266 e/Å3
Displacement parametersBiso mean: 49.4 Å2
Baniso -1Baniso -2Baniso -3
1--10.37 Å20 Å28.28 Å2
2--5.04 Å20 Å2
3---5.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9386 0 46 242 9674
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.711.5
X-RAY DIFFRACTIONc_mcangle_it9.932
X-RAY DIFFRACTIONc_scbond_it9.152
X-RAY DIFFRACTIONc_scangle_it12.722.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.393 489 10.5 %
Rwork0.309 4183 -
obs--69.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARH_LEE.PROTOPH_LEE.PRO
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.393 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.309

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