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- PDB-6jun: MsDpo4-DNA complex 3 -

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Basic information

Entry
Database: PDB / ID: 6jun
TitleMsDpo4-DNA complex 3
Components
  • DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3')
  • DNA polymerase IV
KeywordsREPLICATION/DNA / DNA polymerase / REPLICATION / REPLICATION-DNA complex
Function / homology
Function and homology information


DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / magnesium ion binding / cytoplasm
Similarity search - Function
: / DNA polymerase-iota, thumb domain / DNA polymerase IV / : / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. ...: / DNA polymerase-iota, thumb domain / DNA polymerase IV / : / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-0KX / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
Mycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsNair, D.T. / Johnson, M.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India)Intramural India
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: A polar filter in DNA polymerases prevents ribonucleotide incorporation.
Authors: Johnson, M.K. / Kottur, J. / Nair, D.T.
History
DepositionApr 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: DNA polymerase IV
H: DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3')
G: DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3')
A: DNA polymerase IV
C: DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3')
B: DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,23112
Polymers99,2026
Non-polymers1,0306
Water1,02757
1
F: DNA polymerase IV
H: DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3')
G: DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1166
Polymers49,6013
Non-polymers5153
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-48 kcal/mol
Surface area18850 Å2
MethodPISA
2
A: DNA polymerase IV
C: DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3')
B: DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1166
Polymers49,6013
Non-polymers5153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-54 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.920, 81.320, 210.210
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 polymerase IV / Pol IV


Mass: 38583.789 Da / Num. of mol.: 2 / Mutation: L14Y, C47T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Gene: MSMEG_1014, MSMEG_2294 / Variant: ATCC 700084 / mc(2)155 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QR77, DNA-directed DNA polymerase
#2: DNA chain
DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3')


Mass: 5508.553 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA primer / Source: (synth.) Mycobacterium smegmatis (bacteria)
#3: Chemical ChemComp-0KX / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine


Mass: 466.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H17N4O12P3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 2kMME, Bis Tris Propane ph 6.0, NaCl / PH range: 6 / Temp details: 295 K

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.1272 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 2.51→81.32 Å / Num. obs: 32439 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.9
Reflection shellResolution: 2.51→2.65 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4582 / CC1/2: 0.547 / % possible all: 98.3

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHENIXrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JUL

6jul


Resolution: 2.51→75.843 Å / SU ML: 0.37 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 28.71
RfactorNum. reflection% reflection
Rfree0.257 1618 5 %
Rwork0.2212 --
obs0.223 32341 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.51→75.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5300 778 60 57 6195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046334
X-RAY DIFFRACTIONf_angle_d0.6658798
X-RAY DIFFRACTIONf_dihedral_angle_d12.9743652
X-RAY DIFFRACTIONf_chiral_restr0.0431020
X-RAY DIFFRACTIONf_plane_restr0.0051000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.58390.37871120.31832492X-RAY DIFFRACTION98
2.5839-2.66730.35611230.30022488X-RAY DIFFRACTION99
2.6673-2.76260.40691320.30952494X-RAY DIFFRACTION99
2.7626-2.87320.31531430.31062524X-RAY DIFFRACTION99
2.8732-3.0040.33561300.26952549X-RAY DIFFRACTION100
3.004-3.16240.32791480.26052518X-RAY DIFFRACTION100
3.1624-3.36050.32721650.25162526X-RAY DIFFRACTION100
3.3605-3.620.2781310.2312565X-RAY DIFFRACTION100
3.62-3.98430.22171370.20442547X-RAY DIFFRACTION100
3.9843-4.56070.2031090.1722631X-RAY DIFFRACTION100
4.5607-5.74570.241400.19092621X-RAY DIFFRACTION100
5.7457-75.87730.18631480.1982768X-RAY DIFFRACTION100

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