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- PDB-1ta8: Structural rearrangement accompanying NAD+ synthesis within a bac... -

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Basic information

Entry
Database: PDB / ID: 1ta8
TitleStructural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal
ComponentsDNA ligase, NAD-dependent
KeywordsLIGASE / Nucleotidyl transferase fold
Function / homology
Function and homology information


DNA ligase (NAD+) / DNA ligase (NAD+) activity / base-excision repair, DNA ligation / DNA replication / 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 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Dna Ligase; domain 1 / Helix Hairpins / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / DNA ligase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGajiwala, K.S. / Pinko, C.
Citation
Journal: STRUCTURE / Year: 2004
Title: Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal.
Authors: Gajiwala, K.S. / Pinko, C.
#1: Journal: Structure / Year: 1999
Title: Structure of the adenylation domain of an NAD dependent DNA ligase
Authors: Singleton, M.R. / Hakansson, K. / Timson, D.J. / Wigley, D.B.
#2: Journal: 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
DepositionMay 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: DNA ligase, NAD-dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6055
Polymers37,9861
Non-polymers6194
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.167, 86.105, 57.108
Angle α, β, γ (deg.)90.00, 100.99, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe contents of the asymmetric unit is the biological unit

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Components

#1: Protein DNA ligase, NAD-dependent


Mass: 37985.652 Da / Num. of mol.: 1 / Fragment: Adenylation domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: ligA / Production host: Escherichia coli (E. coli) / References: UniProt: Q837V6, DNA ligase (NAD+)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O8P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Ammonium sulfate, cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 13K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 9, 2003 / Details: Osmic Confocal Max-Flux Optics
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 39492 / Num. obs: 39373 / % possible obs: 99.95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 21.2 Å2 / Rsym value: 0.051 / Net I/σ(I): 16.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3908 / Rsym value: 0.456 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNX2000.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNX2001.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ligase adenylation domain from Bacillus stearothermophilus (PDB ID: 1B04)

1b04


Resolution: 1.8→24.33 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 586308.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3817 10 %RANDOM
Rwork0.2 ---
all0.203 39473 --
obs0.203 38113 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.0195 Å2 / ksol: 0.429161 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å2-0.73 Å2
2--5.2 Å20 Å2
3----6.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2513 0 38 306 2857
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d2.06
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.282.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 572 10 %
Rwork0.3 5145 -
obs--86.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3SO4.PARAM
X-RAY DIFFRACTION4NMN.PARAM

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