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- PDB-2irx: Crystal Structure of the Polymerase Domain from Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 2irx
TitleCrystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D with GTP and Manganese.
ComponentsDNA ligase-like protein Rv0938/MT0965
KeywordsTRANSFERASE / POLYMERASE / PRIMASE / LIGASE / NHEJ / GTP
Function / homology
Function and homology information


: / ribonucleotide binding / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA ligation / single-stranded DNA 3'-5' DNA exonuclease activity / DNA primase activity / DNA replication, synthesis of primer / DNA-directed 5'-3' RNA polymerase activity ...: / ribonucleotide binding / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA ligation / single-stranded DNA 3'-5' DNA exonuclease activity / DNA primase activity / DNA replication, synthesis of 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
GUANOSINE-5'-TRIPHOSPHATE / : / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBrissett, N.C. / Pitcher, R.S. / Doherty, A.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure and function of a mycobacterial NHEJ DNA repair polymerase.
Authors: Pitcher, R.S. / Brissett, N.C. / Picher, A.J. / Andrade, P. / Juarez, R. / Thompson, D. / Fox, G.C. / Blanco, L. / Doherty, A.J.
History
DepositionOct 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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-like protein Rv0938/MT0965
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4033
Polymers32,8251
Non-polymers5782
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.557, 75.532, 89.518
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-like protein Rv0938/MT0965


Mass: 32825.148 Da / Num. of mol.: 1 / Fragment: LigD Polymerase Domain (residues 1-300)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0938 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P71571, UniProt: P9WNV3*PLUS, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Na Hepes, 0.01M MnCl2, 10%(v/v) iso-propanol, 20% PEG 4000, 0.01M GTP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 10, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→34.79 Å / Num. obs: 27079 / % possible obs: 98.4 % / Observed criterion σ(I): -3.7 / Redundancy: 9 % / Biso Wilson estimate: 21.30639 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.067 / Net I/σ(I): 26.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3490 / Rsym value: 0.478 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→34.79 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.321 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20943 1360 5 %RANDOM
Rwork0.16418 ---
obs0.16646 25666 98.4 %-
all-27026 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.446 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 33 327 2524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222248
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9843078
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0075282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43522.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20315347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.391521
X-RAY DIFFRACTIONr_chiral_restr0.0920.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021696
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21115
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21500
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7951.51455
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21622281
X-RAY DIFFRACTIONr_scbond_it1.9963927
X-RAY DIFFRACTIONr_scangle_it3.0174.5797
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 86 -
Rwork0.297 1476 -
obs-1476 78.1 %
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)
13.71960.8714-1.74298.1576-7.110412.7579-0.12210.311-0.032-0.59410.25820.21430.2601-0.1568-0.13610.0268-0.0266-0.01760.074-0.040.074916.616315.3522-5.4902
20.72370.2819-0.31830.92060.00880.803-0.03470.0846-0.0478-0.09230.0384-0.0046-0.01010.0044-0.00360.0324-0.001-0.00810.0726-0.00930.055720.361125.5495-0.2749
317.00260.95631.298216.38431.57528.1551-0.837-0.25321.2743-0.0540.387-1.7506-0.78211.20910.4501-0.0154-0.0871-0.00270.1210.0180.105933.865837.9889-10.6655
40.26680.5369-0.21271.52190.08870.7739-0.03340.160.0161-0.14010.03850.0462-0.1351-0.0083-0.00510.0447-0.0066-0.00070.07750.00250.046821.004731.7227-5.0174
51.68790.2032-0.20582.06040.77472.85720.1042-0.01010.1782-0.20160.00910.0386-0.27030.0898-0.11320.14710.00210.00860.0442-0.0130.114220.799846.06396.7834
62.33211.0275-0.71711.51440.79831.82960.11730.13310.3719-0.2016-0.00010.2835-0.561-0.0646-0.11710.1430.03340.00560.0142-0.00470.071416.696748.09686.9439
70.73430.96370.85982.91910.50479.8329-0.0154-0.05260.054-0.23080.0809-0.3250.07010.5863-0.06550.0523-0.02950.02010.0462-0.03280.070128.718551.289715.9367
80.76530.3325-0.00481.6990.38210.79040.0373-0.15180.05980.1011-0.0380.0772-0.12470.03110.00070.05690.00120.00840.0617-0.00970.04218.396138.14411.2135
93.2820.7145-0.47281.93870.11631.8386-0.0273-0.04350.1956-0.0146-0.03480.3134-0.1546-0.38690.06210.02260.02660.00410.0814-0.03830.08067.019234.84228.3037
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 1910 - 19
2X-RAY DIFFRACTION2AA20 - 8020 - 80
3X-RAY DIFFRACTION3AA81 - 9081 - 90
4X-RAY DIFFRACTION4AA91 - 12091 - 120
5X-RAY DIFFRACTION5AA121 - 162121 - 162
6X-RAY DIFFRACTION6AA163 - 192163 - 192
7X-RAY DIFFRACTION7AA193 - 227193 - 227
8X-RAY DIFFRACTION8AA228 - 268228 - 268
9X-RAY DIFFRACTION9AA269 - 292269 - 292

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