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- PDB-7obn: Structural investigations of a new L3 DNA ligase: structure-funct... -

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Basic information

Entry
Database: PDB / ID: 7obn
TitleStructural investigations of a new L3 DNA ligase: structure-function analysis
Components
  • DNA (5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')
  • DNA ligase
  • DNA/RNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC))-D(P*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')
KeywordsDNA BINDING PROTEIN / DNA ligase / structure-function analysis
Function / homologyADENOSINE MONOPHOSPHATE / DNA / DNA (> 10)
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLeiros, H.-K.S. / Williamson, A.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden Fund18-UOW-034 A.W New Zealand
CitationJournal: Sci Rep / Year: 2021
Title: Bacteriophage origin of some minimal ATP-dependent DNA ligases: a new structure from Burkholderia pseudomallei with striking similarity to Chlorella virus ligase.
Authors: Pan, J. / Lian, K. / Sarre, A. / Leiros, H.S. / Williamson, A.
History
DepositionApr 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 1, 2025Group: Derived calculations / Structure summary / Category: pdbx_entry_details / struct_conn / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')
C: DNA/RNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC))-D(P*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')
A: DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0185
Polymers48,5753
Non-polymers4432
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-52 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.473, 45.552, 111.459
Angle α, β, γ (deg.)90.000, 103.939, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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DNA chain , 2 types, 2 molecules BC

#1: DNA chain DNA (5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')


Mass: 6494.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA / Source: (synth.) Escherichia coli (E. coli)
#2: DNA chain DNA/RNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC))-D(P*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')


Mass: 6422.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ATTGCGAC(OMC)CCACTATCGGAA / Source: (synth.) Escherichia coli (E. coli)

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Protein , 1 types, 1 molecules A

#3: Protein DNA ligase


Mass: 35658.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 62 molecules

#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 26% PEG 3350, 100 mM Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.45→48.31 Å / Num. obs: 22036 / % possible obs: 96.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 56.09 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.056 / Net I/σ(I): 7.9
Reflection shellResolution: 2.45→2.55 Å / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2031 / CC1/2: 0.578 / Rpim(I) all: 0.724 / % possible all: 72.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2q2t

2q2t


Resolution: 2.45→24.62 Å / SU ML: 0.4313 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.9236
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.283 2022 9.2 %
Rwork0.2567 19948 -
obs0.259 21970 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.73 Å2
Refinement stepCycle: LAST / Resolution: 2.45→24.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2349 857 27 60 3293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01153403
X-RAY DIFFRACTIONf_angle_d1.89184779
X-RAY DIFFRACTIONf_chiral_restr0.0737514
X-RAY DIFFRACTIONf_plane_restr0.0129475
X-RAY DIFFRACTIONf_dihedral_angle_d30.2849748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.510.40211240.37971127X-RAY DIFFRACTION76.09
2.51-2.580.35961070.36721241X-RAY DIFFRACTION84.67
2.58-2.650.36741530.35831401X-RAY DIFFRACTION95.4
2.66-2.740.41821640.38441421X-RAY DIFFRACTION99.44
2.74-2.840.39161420.34131486X-RAY DIFFRACTION99.69
2.84-2.950.35041400.31981444X-RAY DIFFRACTION98.75
2.95-3.090.35351510.31821446X-RAY DIFFRACTION97.56
3.09-3.250.31351520.2841467X-RAY DIFFRACTION99.08
3.25-3.450.29091610.25251445X-RAY DIFFRACTION99.2
3.45-3.720.28391420.26591477X-RAY DIFFRACTION98.54
3.72-4.090.28541410.24441463X-RAY DIFFRACTION98.59
4.09-4.680.23911520.19931475X-RAY DIFFRACTION99.33
4.68-5.880.22951470.22521498X-RAY DIFFRACTION99.1
5.88-24.620.22841460.22161557X-RAY DIFFRACTION98.67
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)
11.8261870792-1.13899055462-0.2255052738860.5756606304090.3005057544460.555240065744-0.1364639892130.09387233339320.496335503265-0.06286189299160.06479858558720.1464915950530.160164474801-1.031812453720.0001905956679320.3578863267070.139424091886-0.0273355322980.6623017867140.01825777518350.597559004324-49.8624769757-8.9927258373823.9581960978
21.19109785072-0.2173289230421.320929811250.620984597565-0.165282260751.16465233607-0.808705938799-0.745457881567-0.819746877332-0.3007199671990.950694590782-0.765856006871-0.1487294999431.62852582955-0.09094406349050.3187386174920.4527968715960.1007065611281.43591922722-0.07903102359910.868819253322-18.5076891923-16.281805099425.6424778157
33.22954983041-0.3835943848521.146954818930.467261508465-0.6620551988291.010591352510.3274877300840.7598365027320.06699520253760.366270524462-0.344409985101-0.904635524721-0.4211026410250.578012196186-0.02462879819570.4430494598360.436931785502-0.06094149756611.06366602533-0.1013061510640.777234217191-18.7262565314-16.587639784326.3694919871
43.486080234260.121941479162-1.162215871711.52333331691-0.404642817781.65166255326-0.043717102059-0.2692333104410.859675919576-0.01859573505750.08193372009940.69081811005-0.117046138204-0.6424920857840.02223167490170.348045468790.05274328578850.09712780206690.5837133705690.01077377778390.707678585056-50.9465270577-8.4842553263523.1732221597
50.593771891067-0.145343300298-0.39844105711.811594056440.5244442414412.802283785410.0996662497222-0.3403174842350.04982936573420.5277249211520.122891053351-0.07429800622490.4171144663030.535163858911-0.01863387257820.6373831006010.160790771067-0.1245785808390.4634931227980.007075411425580.36406184821-35.0902345048-7.8523696722842.0174520224
61.06392281339-0.44947599392-0.6215141378891.729389973630.9557344015920.9918153455050.386919070481-0.2841726252250.1638242974891.634720977160.177244250613-0.6907488845751.127086232471.17217323380.2057322895340.6211840002290.289076135016-0.359853290571.07525138633-0.01398042573840.389760963759-23.10949839-8.7073826444745.1449128865
71.90791350967-0.269253421875-1.06122744373.802294536010.939730879922.967296747770.22965408271-0.3742806816570.2353156710590.6304906275440.0987029302586-0.0225527585733-0.6332395904850.298201166254-0.1270177613870.726704533925-0.01291468228180.01324486911730.420984337807-0.009146100073530.338399274361-37.94865275270.63424036336246.1689621671
81.848561033990.16240110003-0.4567284893513.3463229312-0.2450805048453.874815718350.00062076490478-0.1758578280160.0255323365141-0.1516586554480.0638321195604-0.2304204070270.0379880586180.2145524667050.02980140672310.3984071412920.03670993646660.03995449972710.30208256202-0.003879083162510.335294293191-30.7667651085-3.6188494558513.2720737475
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1 through 10 )BA1 - 10
22chain 'B' and (resid 11 through 21 )BA11 - 21
33chain 'C' and (resid 22 through 32 )CB22 - 32
44chain 'C' and (resid 33 through 42 )CB33 - 42
55chain 'A' and (resid 2 through 59 )AD2 - 591 - 58
66chain 'A' and (resid 60 through 102 )AD60 - 10259 - 97
77chain 'A' and (resid 103 through 200 )AD103 - 20098 - 186
88chain 'A' and (resid 201 through 318 )AD201 - 318187 - 300

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