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- PDB-3pky: Polymerase Domain from Mycobacterium tuberculosis Ligase D in com... -

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Basic information

Entry
Database: PDB / ID: 3pky
TitlePolymerase Domain from Mycobacterium tuberculosis Ligase D in complex with DNA, UTP and Manganese.
Components
  • DNA 5'-D(*G*CP*CP*GP*CP*AP*AP*CP*GP*CP*AP*CP*G)-3'
  • DNA 5'-D(P*GP*CP*GP*GP*C)-3'
  • Putative DNA ligase-like protein
KeywordsTRANSFERASE/DNA / protein-DNA complex / transferase-DNA complex / Nucleotide-binding / polymerase / primase / transferase / NHEJ
Function / homology
Function and homology information


: / ribonucleotide binding / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / single-stranded DNA 3'-5' DNA exonuclease activity / DNA ligation / DNA primase activity / DNA replication, synthesis of RNA primer / DNA-directed 5'-3' RNA polymerase activity ...: / ribonucleotide binding / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / single-stranded DNA 3'-5' DNA exonuclease activity / DNA ligation / DNA primase activity / DNA replication, synthesis of RNA primer / DNA-directed 5'-3' RNA polymerase activity / double-strand break repair via nonhomologous end joining / double-strand break repair / manganese ion binding / DNA recombination / DNA-directed DNA polymerase activity / nucleotide binding / magnesium ion binding / DNA binding / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Alpha-Beta Plaits - #3300 / LigD polymerase domain, MtLigD-type / DNA ligase D, ligase domain / LigD, primase-polymerase domain / DNA ligase D, polymerase domain / DNA ligase D, 3'-phosphoesterase domain / DNA polymerase Ligase (LigD) / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / ATP-dependent DNA ligase family profile. ...Alpha-Beta Plaits - #3300 / LigD polymerase domain, MtLigD-type / DNA ligase D, ligase domain / LigD, primase-polymerase domain / DNA ligase D, polymerase domain / DNA ligase D, 3'-phosphoesterase domain / DNA polymerase Ligase (LigD) / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / URIDINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / Multifunctional non-homologous end joining DNA repair protein LigD / Multifunctional non-homologous end joining DNA repair protein LigD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsBrissett, N.C. / Fox, G.C. / Pitcher, R.S. / Doherty, A.J.
CitationJournal: Mol.Cell / Year: 2011
Title: Structure of a Preternary Complex Involving a Prokaryotic NHEJ DNA Polymerase.
Authors: Brissett, N.C. / Martin, M.J. / Pitcher, R.S. / Bianchi, J. / Juarez, R. / Green, A.J. / Fox, G.C. / Blanco, L. / Doherty, A.J.
History
DepositionNov 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Putative DNA ligase-like protein
B: Putative DNA ligase-like protein
C: DNA 5'-D(P*GP*CP*GP*GP*C)-3'
D: DNA 5'-D(*G*CP*CP*GP*CP*AP*AP*CP*GP*CP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,30610
Polymers71,1184
Non-polymers1,1886
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.711, 145.711, 44.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114B6 - 290
2114A6 - 290

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative DNA ligase-like protein


Mass: 32825.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: MT0965, MTCY08D9.01c, MTCY10D7.36c, Rv0938 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P71571, UniProt: P9WNV3*PLUS, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA 5'-D(P*GP*CP*GP*GP*C)-3'


Mass: 1521.024 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA 5'-D(*G*CP*CP*GP*CP*AP*AP*CP*GP*CP*AP*CP*G)-3'


Mass: 3946.577 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 53 molecules

#4: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.36 Å3/Da / Density % sol: 63.34 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20%(w/v)PEG 3350, 0.2 M Ammonium chloride, 10mM MnCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 28, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3.1→48.57 Å / Num. obs: 17593 / % possible obs: 99.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.161 / Rsym value: 0.161 / Χ2: 1.414 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.1-3.214.40.67917301.05697.5
3.21-3.345.60.56917001.16899.9
3.34-3.4960.40917661.206100
3.49-3.6860.31217511.244100
3.68-3.915.90.2417461.40899.9
3.91-4.215.80.1817491.353100
4.21-4.635.60.13617761.48399.9
4.63-5.35.50.11917521.54299.9
5.3-6.675.60.11218111.55599.9
6.67-504.90.08118122.13497.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.13 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å38.26 Å
Translation4 Å38.26 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→48.57 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.191 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8242 / SU B: 37 / SU ML: 0.32 / SU R Cruickshank DPI: 0.3502 / SU Rfree: 0.415 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 897 5.1 %RANDOM
Rwork0.1907 ---
obs0.1936 17577 99.32 %-
all-16680 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.99 Å2 / Biso mean: 71.3414 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4377 209 62 47 4695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224770
X-RAY DIFFRACTIONr_angle_refined_deg1.2972.0376567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32422.678183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.12215698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.051542
X-RAY DIFFRACTIONr_chiral_restr0.0770.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213540
X-RAY DIFFRACTIONr_mcbond_it0.3881.52865
X-RAY DIFFRACTIONr_mcangle_it0.73824622
X-RAY DIFFRACTIONr_scbond_it1.01231905
X-RAY DIFFRACTIONr_scangle_it1.8314.51945
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 2172 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.210.5
MEDIUM THERMAL0.182
LS refinement shellResolution: 3.098→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 68 -
Rwork0.285 1192 -
all-1260 -
obs--96.33 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.750.55081.04583.6641.11893.7442-0.1212-0.0457-0.0235-0.15980.1280.1876-0.17840.1814-0.00680.017-0.0191-0.01940.04860.05150.07447.12160.1951.579
23.55520.48441.06742.72290.94964.10590.1243-0.11730.2102-0.0506-0.1206-0.00030.1948-0.1641-0.00360.045-0.01730.04950.0147-0.02040.079312.58825.694-9.623
312.88988.3703-2.75915.9352-3.31655.3361-0.6818-0.12060.0831-0.7355-0.481-0.27941.07331.10581.16280.35730.14980.08410.53560.08140.700827.2541.699-11.652
42.37233.5322-1.877310.90190.523.4469-0.5536-0.5565-0.09750.49120.03560.46371.19020.93280.5180.49470.28550.0950.3949-0.05250.643531.1546.2634.193
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 290
2X-RAY DIFFRACTION2B6 - 290
3X-RAY DIFFRACTION3A1 - 303
4X-RAY DIFFRACTION4B1 - 303

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