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- PDB-1b04: STRUCTURE OF THE ADENYLATION DOMAIN OF AN NAD+ DEPENDENT LIGASE -

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Basic information

Entry
Database: PDB / ID: 1b04
TitleSTRUCTURE OF THE ADENYLATION DOMAIN OF AN NAD+ DEPENDENT LIGASE
ComponentsPROTEIN (DNA LIGASE)
KeywordsLIGASE / DNA REPLICATION
Function / homology
Function and homology information


DNA ligase (NAD+) / DNA ligase (NAD+) activity / DNA replication / DNA repair / DNA binding / metal ion binding
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 / 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 / Dna Ligase; domain 1 / Helix Hairpins / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsSingleton, M.R. / Hakansson, K. / Timson, D.J. / Wigley, D.B.
CitationJournal: Structure Fold.Des. / 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.
History
DepositionNov 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (DNA LIGASE)
B: PROTEIN (DNA LIGASE)


Theoretical massNumber of molelcules
Total (without water)71,6652
Polymers71,6652
Non-polymers00
Water3,423190
1
A: PROTEIN (DNA LIGASE)


Theoretical massNumber of molelcules
Total (without water)35,8321
Polymers35,8321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (DNA LIGASE)


Theoretical massNumber of molelcules
Total (without water)35,8321
Polymers35,8321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.720, 95.720, 225.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsTHE PROTEIN MONOMER IS BELIEVED TO BE THE PHYSIOLOGICALLY ACTIVE SPECIES

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Components

#1: Protein PROTEIN (DNA LIGASE) / EC 6.5.1.2


Mass: 35832.352 Da / Num. of mol.: 2 / Fragment: ADENYLATION DOMAIN / Mutation: K114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: NCA 1503 / Gene: LIG / Plasmid: PET21D / Species (production host): Escherichia coli / Gene (production host): LIG / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O87703, DNA ligase (NAD+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.6 Å3/Da / Density % sol: 65 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal
*PLUS
Density % sol: 65 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mMTris-HCl1drop
31 mMdithiothreitol1drop
4100 mM1reservoirNaOAc
51.5 mM1reservoirCo(NH3)6Cl3
60.6 M1reservoirMgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 25982 / % possible obs: 97.5 % / Redundancy: 2.8 % / Rsym value: 0.09 / Net I/σ(I): 8.9
Reflection shellResolution: 2.8→2.9 Å / Rsym value: 0.308 / % possible all: 99.2
Reflection
*PLUS
Rmerge(I) obs: 0.09

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1301 5 %RANDOM
Rwork0.23 ---
obs0.23 25982 97.4 %-
Displacement parametersBiso mean: 47.4 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4936 0 0 190 5126
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0560.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0610.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.1222
X-RAY DIFFRACTIONp_mcangle_it3.63
X-RAY DIFFRACTIONp_scbond_it2.4622
X-RAY DIFFRACTIONp_scangle_it4.0573
X-RAY DIFFRACTIONp_plane_restr0.02660.03
X-RAY DIFFRACTIONp_chiral_restr0.1930.15
X-RAY DIFFRACTIONp_singtor_nbd0.2210.3
X-RAY DIFFRACTIONp_multtor_nbd0.2820.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2180.3
X-RAY DIFFRACTIONp_planar_tor4.37
X-RAY DIFFRACTIONp_staggered_tor24.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.420
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.23 / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_plane_restr0.03
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_scbond_it2
X-RAY DIFFRACTIONp_mcangle_it3
X-RAY DIFFRACTIONp_scangle_it3

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