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- PDB-2far: Crystal Structure of Pseudomonas aeruginosa LigD polymerase domai... -

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Basic information

Entry
Database: PDB / ID: 2far
TitleCrystal Structure of Pseudomonas aeruginosa LigD polymerase domain with dATP and Manganese
Componentsprobable ATP-dependent DNA ligase
KeywordsHydrolase/Transferase / polymerase / primase / ligase / NHEJ / dATP / Hydrolase-Transferase COMPLEX
Function / homology
Function and homology information


RNA exonuclease activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA biosynthetic process / nucleotidyltransferase activity / DNA recombination / DNA-directed DNA polymerase activity / DNA repair / DNA binding / ATP binding / metal ion binding
Similarity search - Function
DNA ligase D / LigD polymerase domain, PaeLigD-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 primase, PRIM domain / DNA primase, PRIM domain / DNA ligase, ATP-dependent, C-terminal ...DNA ligase D / LigD polymerase domain, PaeLigD-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 primase, PRIM domain / DNA primase, PRIM domain / 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 / Nucleic acid-binding, OB-fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / : / Multifunctional non-homologous end joining protein LigD
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhu, H. / Nandakumar, J. / Aniukwu, J. / Wang, L.K. / Glickman, M.S. / Lima, C.D. / Shuman, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D
Authors: Zhu, H. / Nandakumar, J. / Aniukwu, J. / Wang, L.K. / Glickman, M.S. / Lima, C.D. / Shuman, S.
History
DepositionDec 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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 / 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_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.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_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.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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: probable ATP-dependent DNA ligase
B: probable ATP-dependent DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,87711
Polymers68,3862
Non-polymers1,4909
Water8,917495
1
A: probable ATP-dependent DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9866
Polymers34,1931
Non-polymers7935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: probable ATP-dependent DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8905
Polymers34,1931
Non-polymers6974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.736, 203.787, 44.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein probable ATP-dependent DNA ligase


Mass: 34193.156 Da / Num. of mol.: 2 / Fragment: Polymerase domain, residues 533-840
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PSMT3, PET28B derived / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: Q9I1X7
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate, 0.2 M sodium acetate, 5 mM DTT, 26-32% polyethylene glycol-8000, 10 mM Manganous Chloride, 5 mM dATP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2005
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochrometer
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→41.54 Å / Num. all: 98597 / Num. obs: 98203 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 29.9
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 18.3 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FAO

2fao


Resolution: 1.9→41.54 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2142724.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 4886 5 %RANDOM
Rwork0.195 ---
obs0.195 98119 99.5 %-
all-98612 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.8625 Å2 / ksol: 0.389503 e/Å3
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.01 Å
Refinement stepCycle: LAST / Resolution: 1.9→41.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 0 79 495 5216
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.592
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 822 5.1 %
Rwork0.195 15391 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4datp.pardatp.top

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