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- PDB-1vs0: Crystal Structure of the Ligase Domain from M. tuberculosis LigD ... -

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Basic information

Entry
Database: PDB / ID: 1vs0
TitleCrystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A
ComponentsPutative DNA ligase-like protein Rv0938/MT0965
KeywordsLIGASE / OB fold / nucleotidyl transferase / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


: / ribonucleotide binding / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA ligation / DNA primase activity / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication, synthesis of primer / double-strand break repair via nonhomologous end joining ...: / ribonucleotide binding / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA ligation / DNA primase activity / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication, synthesis of primer / double-strand break repair via nonhomologous end joining / DNA-directed 5'-3' RNA polymerase activity / 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
LigD polymerase domain, MtLigD-type / DNA ligase D, ligase domain / DNA ligase D, polymerase domain / : / LigD, primase-polymerase domain / DNA ligase D, 3'-phosphoesterase domain / DNA polymerase Ligase (LigD) / Dna Ligase; domain 1 - #70 / DNA ligase/mRNA capping enzyme / DNA ligase, ATP-dependent, C-terminal ...LigD polymerase domain, MtLigD-type / DNA ligase D, ligase domain / DNA ligase D, polymerase domain / : / LigD, primase-polymerase domain / DNA ligase D, 3'-phosphoesterase domain / DNA polymerase Ligase (LigD) / Dna Ligase; domain 1 - #70 / DNA ligase/mRNA capping enzyme / 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 / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
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 / MAD / Resolution: 2.4 Å
AuthorsAkey, D. / Martins, A. / Aniukwu, J. / Glickman, M.S. / Shuman, S. / Berger, J.M. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure and Nonhomologous End-joining Function of the Ligase Component of Mycobacterium DNA Ligase D.
Authors: Akey, D. / Martins, A. / Aniukwu, J. / Glickman, M.S. / Shuman, S. / Berger, J.M.
History
DepositionJan 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative DNA ligase-like protein Rv0938/MT0965
B: Putative DNA ligase-like protein Rv0938/MT0965
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,89911
Polymers69,4712
Non-polymers4289
Water7,332407
1
A: Putative DNA ligase-like protein Rv0938/MT0965
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9616
Polymers34,7351
Non-polymers2265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative DNA ligase-like protein Rv0938/MT0965
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9375
Polymers34,7351
Non-polymers2024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.102, 57.102, 368.957
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a monomer. There are two monomers in the asymmetric unit.

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Components

#1: Protein Putative DNA ligase-like protein Rv0938/MT0965


Mass: 34735.379 Da / Num. of mol.: 2 / Fragment: LigD ligase domain
Source method: isolated from a genetically manipulated source
Details: Adenylated form / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Description: TEV cleavable His tag / Gene: Rv0938, MT0965 / Plasmid: pAEB1120 / Production host: Escherichia coli (E. coli) / Strain (production host): pLysS / References: UniProt: P71571, UniProt: P9WNV3*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 6% PEG 3000, 25 mM ZnCl2, 100 mM sodium acetate (pH 4.6), VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9796, 1.020, 0.9798
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 23, 2004
RadiationMonochromator: ALS Beamline 8.3.1 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
21.021
30.97981
ReflectionResolution: 2.4→50 Å / Num. all: 28934 / Num. obs: 28772 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rsym value: 0.082 / Net I/σ(I): 18.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 5147 / Rsym value: 0.35 / % possible all: 96.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data reduction
SOLVEphasing
REFMAC5.2refinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / SU B: 14.811 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.414 / ESU R Free: 0.264
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1453 5.1 %RANDOM
Rwork0.192 ---
all0.195 28934 --
obs0.195 28487 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.715 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20.51 Å20 Å2
2--1.01 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4777 0 9 407 5193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214881
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9666636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8145616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01522.466219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.65415770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2041551
X-RAY DIFFRACTIONr_chiral_restr0.1040.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023793
X-RAY DIFFRACTIONr_nbd_refined0.2330.22107
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23226
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2366
X-RAY DIFFRACTIONr_metal_ion_refined0.3090.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.2131
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3520.229
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1370.27
X-RAY DIFFRACTIONr_mcbond_it2.4973.53090
X-RAY DIFFRACTIONr_mcangle_it3.71554836
X-RAY DIFFRACTIONr_scbond_it2.2813.52060
X-RAY DIFFRACTIONr_scangle_it3.073.51799
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 111 -
Rwork0.244 1894 -
obs-2005 97 %
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)
10.1221-0.0542-0.0150.74150.36661.22-0.01830.0440.02430.0298-0.060.01110.006-0.02710.0783-0.06230.03250.0163-0.07580.0108-0.02-6.607752.996125.3335
21.0544-0.3731-0.23592.24261.96521.94580.07530.00730.03160.4854-0.14550.01480.32770.08360.07020.1044-0.05210.0742-0.1325-0.0023-0.0717-15.784975.2068154.8358
31.88181.1439-0.65490.8552-0.01631.13950.1567-0.09560.04240.1717-0.08960.07620.00740.1108-0.06710.0798-0.14430.0624-0.1107-0.0371-0.08696.687155.7937188.1162
40.41840.34640.0471.04670.04612.85640.0112-0.0464-0.093-0.12610.06970.0411-0.17680.0775-0.0809-0.0295-0.0530.0234-0.0626-0.0266-0.062-17.928142.1284214.3944
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA453 - 6384 - 189
22AA639 - 759190 - 310
33BB453 - 6384 - 189
44BB639 - 759190 - 310

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