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- PDB-9fzx: Rhizobium phage ligase -

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Basic information

Entry
Database: PDB / ID: 9fzx
TitleRhizobium phage ligase
Components
  • DNA
  • DNA (5'-D(*TP*TP*CP*CP*GP*AP*CP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')
  • DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')
  • DNA ligase
KeywordsLIGASE / Rhizobioum phage ligase
Function / homology
Function and homology information


DNA ligase (ATP) activity / DNA recombination / DNA replication / DNA repair / ATP binding
Similarity search - Function
DNA ligase, OB-like domain / DNA ligase OB-like domain / : / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DNA / DNA (> 10) / DNA ligase
Similarity search - Component
Biological speciesRhizobium phage 16-3 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.196 Å
AuthorsRothweiler, U. / Williamson, A.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway Norway
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Crystal structure of ATP-dependent DNA ligase from Rhizobium phage vB_RleM_P10VF.
Authors: Rothweiler, U. / Leiros, H.K.S. / Williamson, A.
History
DepositionJul 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,5216
Polymers60,9644
Non-polymers5562
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-33 kcal/mol
Surface area23740 Å2
Unit cell
Length a, b, c (Å)68.039, 100.392, 107.692
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA ligase


Mass: 48107.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium phage 16-3 (virus) / Gene: P10VF_217 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A076YM08

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DNA chain , 3 types, 3 molecules BCD

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


Mass: 6479.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA / Source: (synth.) Rhizobium phage 16-3 (virus)
#3: DNA chain DNA


Mass: 3035.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA / Source: (synth.) Rhizobium phage 16-3 (virus)
#4: DNA chain DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')


Mass: 3342.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA / Source: (synth.) Rhizobium phage 16-3 (virus)

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Non-polymers , 3 types, 186 molecules

#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.21 Å3/Da / Density % sol: 61.63 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / Details: 24% PEG 4000 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: 0.979839 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979839 Å / Relative weight: 1
ReflectionResolution: 2.196→50 Å / Num. obs: 72435 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.99 / Net I/σ(I): 19.56
Reflection shellResolution: 2.2→2.3 Å / Num. unique obs: 11524 / CC1/2: 0.69 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata scaling
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.196→47.4625 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 2089 2.89 %
Rwork0.2051 --
obs0.2063 72380 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.196→47.4625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 857 36 184 4191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034182
X-RAY DIFFRACTIONf_angle_d0.5485817
X-RAY DIFFRACTIONf_dihedral_angle_d13.9712315
X-RAY DIFFRACTIONf_chiral_restr0.039616
X-RAY DIFFRACTIONf_plane_restr0.003602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1963-2.24740.38691340.37094496X-RAY DIFFRACTION96
2.2474-2.30360.3171390.31944693X-RAY DIFFRACTION100
2.3036-2.36580.32071340.27124663X-RAY DIFFRACTION100
2.3658-2.43540.33221410.26114740X-RAY DIFFRACTION100
2.4354-2.51410.27221370.24564707X-RAY DIFFRACTION100
2.5141-2.60390.29091400.24764689X-RAY DIFFRACTION100
2.6039-2.70810.33221460.24394755X-RAY DIFFRACTION100
2.7081-2.83140.2941400.23634689X-RAY DIFFRACTION100
2.8314-2.98060.26011420.23344661X-RAY DIFFRACTION100
2.9806-3.16730.25071460.22164724X-RAY DIFFRACTION100
3.1673-3.41180.2741400.21174644X-RAY DIFFRACTION99
3.4118-3.75510.23881410.19094724X-RAY DIFFRACTION100
3.7551-4.29810.2061400.16674686X-RAY DIFFRACTION100
4.2981-5.41390.1891360.15924721X-RAY DIFFRACTION100
5.4139-47.46250.22721330.19124699X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 41.1119 Å / Origin y: 40.4518 Å / Origin z: 23.2751 Å
111213212223313233
T0.2173 Å2-0.0033 Å20.0248 Å2-0.2896 Å2-0.005 Å2--0.2996 Å2
L0.3237 °20.0384 °20.03 °2-1.5803 °20.1042 °2--1.6289 °2
S0.0377 Å °-0.0318 Å °0.0288 Å °0.0804 Å °-0.0286 Å °0.0352 Å °-0.0597 Å °-0.0396 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

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