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- PDB-6rar: Pmar-Lig_PreS3-Mn -

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Basic information

Entry
Database: PDB / ID: 6rar
TitlePmar-Lig_PreS3-Mn
Components
  • ATP-dependent DNA ligase
  • 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/RNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC))-D(P*C)-3')
KeywordsDNA BINDING PROTEIN / DNA ligase / ATP-dependent / ligase-DNA co-crystal structure / determinants in DNA binding
Function / homology
Function and homology information


DNA ligase (ATP) activity / DNA recombination / DNA replication / DNA repair / ATP binding / metal ion binding
Similarity search - Function
DNA ligase, OB-like domain / DNA ligase OB-like domain / : / DNA ligase/mRNA capping enzyme / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, conserved site / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins ...DNA ligase, OB-like domain / DNA ligase OB-like domain / : / DNA ligase/mRNA capping enzyme / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, conserved site / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / : / DNA / DNA (> 10) / ATP-dependent DNA ligase
Similarity search - Component
Biological speciesProchlorococcus marinus str. MIT 9302 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.785 Å
AuthorsLeiros, H.K.S. / Williamson, A.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway244247, 2015 Norway
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation.
Authors: Williamson, A. / Leiros, H.S.
History
DepositionApr 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id

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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*CP*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*C)-3')
D: DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')
I: ATP-dependent DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2417
Polymers62,7434
Non-polymers4983
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-80 kcal/mol
Surface area25240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.304, 103.315, 68.543
Angle α, β, γ (deg.)90.00, 90.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 3 types, 3 molecules BCD

#1: 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 / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA/RNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC))-D(P*C)-3')


Mass: 3035.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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 / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 1 molecules I

#4: Protein ATP-dependent DNA ligase


Mass: 49886.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus marinus str. MIT 9302 (bacteria)
Gene: EU96_0746 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A2ACP7

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Non-polymers , 4 types, 401 molecules

#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 398 / 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: 3.73 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 17-18% PEG 8K, 100 mM ammonium sulfate, 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: ESRF / Beamline: ID23-1 / Wavelength: 0.991872 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.991872 Å / Relative weight: 1
ReflectionResolution: 1.785→68 Å / Num. obs: 57936 / % possible obs: 88.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 29.1 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.084 / Net I/σ(I): 3.1
Reflection shellResolution: 1.785→1.98 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2897 / CC1/2: 0.604 / Rpim(I) all: 0.425 / % possible all: 59.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6rau

6rau


Resolution: 1.785→24.291 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.43
RfactorNum. reflection% reflection
Rfree0.2639 2875 4.97 %
Rwork0.2325 --
obs0.2341 57870 88.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.785→24.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3433 856 28 398 4715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184583
X-RAY DIFFRACTIONf_angle_d1.186341
X-RAY DIFFRACTIONf_dihedral_angle_d11.5123513
X-RAY DIFFRACTIONf_chiral_restr0.055686
X-RAY DIFFRACTIONf_plane_restr0.005663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.785-1.81420.3855100.358888X-RAY DIFFRACTION2
1.8142-1.84550.360280.3578198X-RAY DIFFRACTION5
1.8455-1.87910.4421120.3385346X-RAY DIFFRACTION9
1.8791-1.91520.3778230.314588X-RAY DIFFRACTION15
1.9152-1.95430.3401450.3055953X-RAY DIFFRACTION24
1.9543-1.99670.2991560.31031290X-RAY DIFFRACTION32
1.9967-2.04320.3344790.29091552X-RAY DIFFRACTION39
2.0432-2.09420.3099860.30141933X-RAY DIFFRACTION48
2.0942-2.15080.29951640.29012553X-RAY DIFFRACTION64
2.1508-2.21410.28191390.27313126X-RAY DIFFRACTION77
2.2141-2.28550.30421840.27373403X-RAY DIFFRACTION85
2.2855-2.36710.31581590.26053781X-RAY DIFFRACTION94
2.3671-2.46180.30242630.26293881X-RAY DIFFRACTION98
2.4618-2.57370.32192430.26433904X-RAY DIFFRACTION98
2.5737-2.70920.27891510.25923954X-RAY DIFFRACTION97
2.7092-2.87870.29492000.26633937X-RAY DIFFRACTION98
2.8787-3.10060.311990.25773944X-RAY DIFFRACTION98
3.1006-3.41180.26141850.22393873X-RAY DIFFRACTION96
3.4118-3.90380.24651910.20383845X-RAY DIFFRACTION95
3.9038-4.91170.21612340.18473923X-RAY DIFFRACTION97
4.9117-24.29350.23672440.21733923X-RAY DIFFRACTION96

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