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Basic information

Entry
Database: PDB / ID: 1tae
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 / DNA replication / DNA repair / 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 / breast cancer carboxy-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / DNA ligase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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. / K Kim, H. / 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 1.3Aug 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_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, NAD-dependent
B: DNA ligase, NAD-dependent
C: DNA ligase, NAD-dependent
D: DNA ligase, NAD-dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,13634
Polymers152,1314
Non-polymers5,00530
Water3,171176
1
A: DNA ligase, NAD-dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2728
Polymers38,0331
Non-polymers1,2407
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA ligase, NAD-dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,39210
Polymers38,0331
Non-polymers1,3599
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA ligase, NAD-dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1767
Polymers38,0331
Non-polymers1,1446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA ligase, NAD-dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2959
Polymers38,0331
Non-polymers1,2638
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
B: DNA ligase, NAD-dependent
hetero molecules

A: DNA ligase, NAD-dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,66418
Polymers76,0652
Non-polymers2,59916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area8310 Å2
ΔGint-243 kcal/mol
Surface area27700 Å2
MethodPISA
6
D: DNA ligase, NAD-dependent
hetero molecules

C: DNA ligase, NAD-dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,47216
Polymers76,0652
Non-polymers2,40714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,y-1/2,-z1
Buried area7750 Å2
ΔGint-197 kcal/mol
Surface area27960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.296, 135.179, 115.797
Angle α, β, γ (deg.)90.00, 102.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA ligase, NAD-dependent


Mass: 38032.688 Da / Num. of mol.: 4 / 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, GenBank: 29375318, DNA ligase (NAD+)
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Ammonium sulfate, cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 9, 2004 / 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: 2.7→25 Å / Num. all: 51184 / Num. obs: 50300 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.84 % / Biso Wilson estimate: 56.4 Å2 / Rsym value: 0.074 / Net I/σ(I): 13.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 4916 / Rsym value: 0.374 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CNX2000.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNX2000.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Domain 1b of NMN bound structure of E. faecalis ligase (PDB ID: 1TA8)

1ta8


Resolution: 2.7→24.77 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 482888.09 / 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
Rfree0.263 4919 10 %RANDOM
Rwork0.202 ---
all0.204 50300 --
obs0.204 48981 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.2795 Å2 / ksol: 0.369729 e/Å3
Displacement parametersBiso mean: 43.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.24 Å20 Å2-8.5 Å2
2--2.43 Å20 Å2
3---5.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.7→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10300 0 298 176 10774
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 783 10.5 %
Rwork0.309 6685 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3NAD.PARAM
X-RAY DIFFRACTION4SO4.PARAM

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