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- PDB-3qwu: Putative ATP-dependent DNA ligase from Aquifex aeolicus. -

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Basic information

Entry
Database: PDB / ID: 3qwu
TitlePutative ATP-dependent DNA ligase from Aquifex aeolicus.
ComponentsDNA ligase
KeywordsLIGASE / structural genomics / PSI-2 / Midwest Center for Structural Genomics / MCSG / Protein Structure Initiative
Function / homology
Function and homology information


Alpha-Beta Plaits - #2160 / Nuclear Transport Factor 2; Chain: A, - #740 / RNA ligase, Pab1020 family / RNA ligase Pab1020, C-terminal domain / Ligase Pab1020 C-terminal region / RNA ligase domain, REL/Rln2 / RNA ligase / DNA ligase/mRNA capping enzyme / D-amino Acid Aminotransferase; Chain A, domain 1 / Nuclear Transport Factor 2; Chain: A, ...Alpha-Beta Plaits - #2160 / Nuclear Transport Factor 2; Chain: A, - #740 / RNA ligase, Pab1020 family / RNA ligase Pab1020, C-terminal domain / Ligase Pab1020 C-terminal region / RNA ligase domain, REL/Rln2 / RNA ligase / DNA ligase/mRNA capping enzyme / D-amino Acid Aminotransferase; Chain A, domain 1 / Nuclear Transport Factor 2; Chain: A, / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / RNA ligase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsOsipiuk, J. / Quartey, P. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Putative ATP-dependent DNA ligase from Aquifex aeolicus.
Authors: Osipiuk, J. / Quartey, P. / Collart, F. / Joachimiak, A.
History
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_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: DNA ligase
B: DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0138
Polymers87,2142
Non-polymers7996
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-65 kcal/mol
Surface area32220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.366, 99.165, 103.278
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


Mass: 43606.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1106 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67191
#2: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: SBC-2 / Detector: CCD / Date: Nov 25, 2003
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.35→49.6 Å / Num. all: 39490 / Num. obs: 39490 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obs% possible all
2.35-2.393.60.4462.0594.4
2.39-2.434.10.42596.1
2.43-2.484.70.43499
2.48-2.535.50.43199.9
2.53-2.596.30.369100
2.59-2.656.80.349100
2.65-2.717.40.278100
2.71-2.797.50.246100
2.79-2.877.50.212100
2.87-2.967.50.175100
2.96-3.077.50.138100
3.07-3.197.50.114100
3.19-3.337.50.094100
3.33-3.517.50.08100
3.51-3.737.40.07100
3.73-4.027.40.063100
4.02-4.427.40.055100
4.42-5.067.30.052100
5.06-6.377.20.05100
6.37-506.80.03899.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vug

2vug


Resolution: 2.35→49.58 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 17.161 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25513 1982 5 %RANDOM
Rwork0.20062 ---
obs0.20339 37342 98.99 %-
all-39324 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.406 Å2
Baniso -1Baniso -2Baniso -3
1--2.54 Å20 Å20 Å2
2---0.43 Å20 Å2
3---2.97 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6083 0 52 127 6262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226362
X-RAY DIFFRACTIONr_bond_other_d0.0010.024561
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.9878578
X-RAY DIFFRACTIONr_angle_other_deg0.927311081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7475754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72224.199331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.782151208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0551543
X-RAY DIFFRACTIONr_chiral_restr0.0980.2902
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021353
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.811.53670
X-RAY DIFFRACTIONr_mcbond_other0.1731.51489
X-RAY DIFFRACTIONr_mcangle_it1.54125946
X-RAY DIFFRACTIONr_scbond_it2.37132692
X-RAY DIFFRACTIONr_scangle_it3.8354.52619
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 131 -
Rwork0.249 2524 -
obs--91.96 %
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)
12.02590.32910.05431.1457-0.37990.35430.01-0.32890.17770.04210.0054-0.0363-0.002-0.0481-0.01540.0693-0.0080.00250.0673-0.03670.034842.813635.228214.6449
21.9947-0.2750.28621.7713-0.2390.1686-0.1247-0.69420.01020.15470.09530.0975-0.0527-0.04110.02940.08070.0309-0.00480.27520.01530.02282.331122.948822.4982
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 367
2X-RAY DIFFRACTION2B3 - 366

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