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- PDB-3sgi: Crystal structure of DNA ligase A BRCT domain deleted mutant of M... -

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Basic information

Entry
Database: PDB / ID: 3sgi
TitleCrystal structure of DNA ligase A BRCT domain deleted mutant of Mycobacterium tuberculosis
ComponentsDNA ligase
KeywordsLIGASE / NAD depndent DNA ligase A
Function / homology
Function and homology information


base-excision repair, DNA ligation / DNA ligase (NAD+) / DNA ligase (NAD+) activity / DNA ligation / peptidoglycan-based cell wall / DNA replication / DNA repair / magnesium ion binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
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 ...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 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding proteins / 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 A / DNA ligase A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKukshal, V. / Ravishankar, R.
CitationJournal: To be Published
Title: Crystal Structure of Domain deleted mutant of Mycobacterium tuberculosis NAD+ dependent DNA ligase capture the AMP cofactor in a new state
Authors: Kukshal, V. / Ravishankar, R.
History
DepositionJun 15, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 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_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0942
Polymers67,7461
Non-polymers3471
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.437, 99.564, 144.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA ligase / / Polydeoxyribonucleotide synthase [NAD+]


Mass: 67746.352 Da / Num. of mol.: 1 / Mutation: BRCT domain deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: lig, ligA, MT3094, MTV012.28c, Rv3014c / Plasmid: mtuLigA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P63973, UniProt: P9WNV1*PLUS, DNA ligase (NAD+)
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IN THIS STUDY IS A C-TERMINAL BRCT DOMAIN DELETED MUTANT.

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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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 12% PEG 8000, 0.1M MES, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 14, 2008
RadiationMonochromator: copper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→49.78 Å / Num. all: 13948 / Num. obs: 12456 / % possible obs: 89.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rsym value: 0.24
Reflection shellResolution: 3.497→3.588 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.74 / % possible all: 94.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZAU

1zau


Resolution: 3.5→49.78 Å / Cor.coef. Fo:Fc: 0.774 / Cor.coef. Fo:Fc free: 0.762 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.731 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3221 435 4.9 %RANDOM
Rwork0.31145 ---
obs0.31196 8530 89.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.192 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å20 Å20 Å2
2---0.88 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 3.5→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3176 0 22 23 3221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213267
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9694446
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5185407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06422.785158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.80815520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6171537
X-RAY DIFFRACTIONr_chiral_restr0.1270.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212531
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4621.52031
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87123265
X-RAY DIFFRACTIONr_scbond_it0.97531236
X-RAY DIFFRACTIONr_scangle_it1.8194.51181
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.497→3.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 29 -
Rwork0.32 630 -
obs--93.08 %

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