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- PDB-7k72: Structure of DNA ligase A from Mycobacterium tuberculosis bound to NAD -

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Basic information

Entry
Database: PDB / ID: 7k72
TitleStructure of DNA ligase A from Mycobacterium tuberculosis bound to NAD
ComponentsDNA ligase A
KeywordsLIGASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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 / magnesium 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 / RuvA domain 2-like / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DNA ligase A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Structure of DNA ligase A from Mycobacterium tuberculosis bound to NAD
Authors: Delker, S.L. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionSep 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA ligase A
B: DNA ligase A
C: DNA ligase A
D: DNA ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,78424
Polymers151,2414
Non-polymers3,54320
Water14,538807
1
A: DNA ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6806
Polymers37,8101
Non-polymers8705
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7997
Polymers37,8101
Non-polymers9886
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6405
Polymers37,8101
Non-polymers8304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6656
Polymers37,8101
Non-polymers8555
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.940, 63.810, 120.730
Angle α, β, γ (deg.)96.220, 89.550, 111.970
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 18 through 19 or (resid 20...
21(chain B and (resid 18 through 29 or (resid 30...
31(chain C and (resid 18 through 29 or (resid 30...
41(chain D and (resid 18 through 22 or (resid 23...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 18 through 19 or (resid 20...A18 - 19
121(chain A and (resid 18 through 19 or (resid 20...A20
131(chain A and (resid 18 through 19 or (resid 20...A17 - 334
141(chain A and (resid 18 through 19 or (resid 20...A17 - 334
151(chain A and (resid 18 through 19 or (resid 20...A17 - 334
161(chain A and (resid 18 through 19 or (resid 20...A17 - 334
211(chain B and (resid 18 through 29 or (resid 30...B18 - 29
221(chain B and (resid 18 through 29 or (resid 30...B30
231(chain B and (resid 18 through 29 or (resid 30...B18 - 334
241(chain B and (resid 18 through 29 or (resid 30...B18 - 334
251(chain B and (resid 18 through 29 or (resid 30...B18 - 334
261(chain B and (resid 18 through 29 or (resid 30...B18 - 334
311(chain C and (resid 18 through 29 or (resid 30...C18 - 29
321(chain C and (resid 18 through 29 or (resid 30...C30
331(chain C and (resid 18 through 29 or (resid 30...C17 - 334
341(chain C and (resid 18 through 29 or (resid 30...C17 - 334
351(chain C and (resid 18 through 29 or (resid 30...C17 - 334
361(chain C and (resid 18 through 29 or (resid 30...C17 - 334
411(chain D and (resid 18 through 22 or (resid 23...D18 - 22
421(chain D and (resid 18 through 22 or (resid 23...D23
431(chain D and (resid 18 through 22 or (resid 23...D17 - 334
441(chain D and (resid 18 through 22 or (resid 23...D17 - 334
451(chain D and (resid 18 through 22 or (resid 23...D17 - 334
461(chain D and (resid 18 through 22 or (resid 23...D17 - 334

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
DNA ligase A / LigA / Polydeoxyribonucleotide synthase [NAD(+)]


Mass: 37810.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ligA, lig, Rv3014c, MTV012.28c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNV1, DNA ligase (NAD+)

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Non-polymers , 5 types, 827 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


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


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 807 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus A12 +4 mM NAD (BSI1606) 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M of each divalent cation (0.3 M magnesium chloride, 0.3 M calcium chloride), 0.1 M bicine/Trizma ...Details: Morpheus A12 +4 mM NAD (BSI1606) 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M of each divalent cation (0.3 M magnesium chloride, 0.3 M calcium chloride), 0.1 M bicine/Trizma base pH 8.5, cryo: direct, MytuD.17946.a.B2.PS38127 at 21.72mg/ml, cryo: direct, tray: 289017A12, puck ydo7-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→44.59 Å / Num. obs: 86267 / % possible obs: 98.1 % / Redundancy: 3.937 % / Biso Wilson estimate: 37.983 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.076 / Χ2: 1.016 / Net I/σ(I): 14.18 / Num. measured all: 339637 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.13.9820.5932.3924988646662750.7840.68597
2.1-2.163.9770.4842.9624536633961700.8360.55997.3
2.16-2.223.9740.3733.9223981621160350.8980.43197.2
2.22-2.293.9750.3074.6523104596058130.9280.35597.5
2.29-2.373.970.2675.3722572582656860.9470.30997.6
2.37-2.453.9690.2276.2521803561454930.960.26397.8
2.45-2.543.960.1827.7321000540853030.9690.21198.1
2.54-2.653.9630.159.1320273521651160.9790.17498.1
2.65-2.763.9570.1211.0819306496848790.9880.13998.2
2.76-2.93.9320.08914.4418670482647480.9930.10398.4
2.9-3.063.9320.07317.4217543452844620.9940.08498.5
3.06-3.243.9230.05820.7716657430042460.9960.06798.7
3.24-3.473.9090.04625.1615524401739710.9970.05398.9
3.47-3.743.890.0428.3314513376737310.9980.04699
3.74-4.13.8770.03631.7613240345834150.9980.04198.8
4.1-4.583.8780.03134.4412092314231180.9980.03699.2
4.58-5.293.8510.03134.610539275327370.9980.03699.4
5.29-6.483.8550.03433.718928233123160.9970.03999.4
6.48-9.173.8170.02836.536798178617810.9980.03399.7
9.17-44.593.6730.02939.9235709849720.9970.03498.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SGI

3sgi


Resolution: 2.05→44.59 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 21.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 1912 2.22 %
Rwork0.1683 84345 -
obs0.1691 86257 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.61 Å2 / Biso mean: 39.4182 Å2 / Biso min: 14.8 Å2
Refinement stepCycle: final / Resolution: 2.05→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9912 0 227 807 10946
Biso mean--32.28 39.94 -
Num. residues----1271
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5435X-RAY DIFFRACTION6.953TORSIONAL
12B5435X-RAY DIFFRACTION6.953TORSIONAL
13C5435X-RAY DIFFRACTION6.953TORSIONAL
14D5435X-RAY DIFFRACTION6.953TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.10.26381410.23215926606797
2.1-2.160.24771300.21625981611197
2.16-2.220.25371450.19925982612797
2.22-2.290.24191690.18435914608398
2.29-2.380.2281290.18026012614198
2.38-2.470.22861520.18295993614598
2.47-2.580.22581060.18166055616198
2.58-2.720.24341270.18726053618098
2.72-2.890.28291460.18726024617098
2.89-3.110.21721500.18146020617099
3.11-3.430.19011310.16426113624499
3.43-3.920.16971220.14886067618999
3.92-4.940.1781250.13456104622999
4.94-44.590.17071390.16426101624099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.031-0.08560.29173.06510.33021.9666-0.03740.1070.17570.13750.06840.1718-0.16430.0189-0.05360.2538-0.03920.01710.33280.04270.1844.2344.7828-46.0142
22.2549-0.069-0.55872.99770.18512.57-0.00160.15080.34-0.01160.1034-0.1817-0.49410.3471-0.09770.2873-0.0942-0.00690.38730.04810.254910.69958.3942-52.2136
33.30280.46431.04582.05790.30622.3761-0.11750.3580.2305-0.30630.0986-0.2189-0.29930.69260.01590.3735-0.0740.0050.62460.00560.226324.613253.2067-77.9337
42.53110.15421.07421.89290.69863.52270.13530.1432-0.25760.0695-0.02350.03760.3690.0533-0.0990.2911-0.05020.01710.3488-0.00690.20918.073436.7291-62.5891
52.68530.7505-0.55392.3392-0.71282.2688-0.16070.5246-0.1534-0.31740.250.10440.1335-0.3772-0.09060.23880.00390.00560.2673-0.03050.1768-6.6029-13.1953-18.0297
64.1578-0.03-0.0982.315-0.30581.46880.01390.06570.07020.01420.07730.33680.0374-0.3098-0.08560.23330.019-0.0080.1798-0.01180.229-9.9035-2.85630.5528
71.74190.87670.03942.9982-0.69422.5788-0.00940.0135-0.00860.0882-0.0351-0.326-0.13240.21290.0570.16650.0422-0.02750.1398-0.02330.260310.8113-2.1786-1.9449
82.41230.6039-0.20391.7560.22751.1330.04170.01660.38130.04460.02560.1297-0.2069-0.0554-0.04260.22330.04240.01360.1292-0.01750.2804-7.33822.77063.4891
92.19260.3025-0.95343.4604-0.14734.3280.1584-0.23560.25110.52550.06590.1909-0.2973-0.3527-0.20250.3243-0.0148-0.00850.3258-0.00880.20210.725141.352723.5815
103.5511-0.95580.89143.16970.02621.49110.05910.01610.20940.0331-0.09530.0966-0.0647-0.17120.04440.21210.00080.02130.1737-0.0090.20766.529634.35743.982
112.44650.2189-0.58113.24920.61532.42860.0412-0.297-0.33860.5739-0.0426-0.15150.55770.14110.07470.37780.01-0.08220.19420.02340.273118.481119.215213.1115
122.7082-0.1581.08222.93930.71872.14880.2155-0.168-0.24390.0972-0.11630.25670.2564-0.228-0.06730.1889-0.0175-0.02230.14860.00060.22485.684727.66821.6103
134.1068-0.6642-0.02283.95391.83234.81370.06170.1015-0.38590.37630.0409-0.09860.48280.647-0.11210.34880.02510.00110.47060.00410.213111.0225-11.3553-34.2805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 66 through 226 )C66 - 226
2X-RAY DIFFRACTION2chain 'C' and (resid 227 through 334 )C227 - 334
3X-RAY DIFFRACTION3chain 'D' and (resid 17 through 92 )D17 - 92
4X-RAY DIFFRACTION4chain 'D' and (resid 93 through 334 )D93 - 334
5X-RAY DIFFRACTION5chain 'A' and (resid 17 through 92 )A17 - 92
6X-RAY DIFFRACTION6chain 'A' and (resid 93 through 142 )A93 - 142
7X-RAY DIFFRACTION7chain 'A' and (resid 143 through 246 )A143 - 246
8X-RAY DIFFRACTION8chain 'A' and (resid 247 through 334 )A247 - 334
9X-RAY DIFFRACTION9chain 'B' and (resid 18 through 92 )B18 - 92
10X-RAY DIFFRACTION10chain 'B' and (resid 93 through 142 )B93 - 142
11X-RAY DIFFRACTION11chain 'B' and (resid 143 through 239 )B143 - 239
12X-RAY DIFFRACTION12chain 'B' and (resid 240 through 334 )B240 - 334
13X-RAY DIFFRACTION13chain 'C' and (resid 17 through 65 )C17 - 65

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