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- PDB-6jus: MsDpo4-DNA complex 6 -

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Basic information

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


SOS response / error-prone translesion synthesis / DNA-templated DNA replication / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol
Similarity search - Function
: / DNA polymerase-iota, thumb domain / DNA polymerase IV / : / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain ...: / DNA polymerase-iota, thumb domain / DNA polymerase IV / : / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / 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 Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-2TM / : / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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: 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 / refine_hist / 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 / _refine_hist.d_res_low / _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
A: DNA polymerase IV
B: DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*G)-3')
C: DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*G)-3')
F: DNA polymerase IV
G: DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*G)-3')
H: DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,28812
Polymers99,1066
Non-polymers1,1826
Water1,60389
1
A: DNA polymerase IV
B: DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*G)-3')
C: DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1446
Polymers49,5533
Non-polymers5913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-45 kcal/mol
Surface area19380 Å2
MethodPISA
2
F: DNA polymerase IV
G: DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*G)-3')
H: DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1446
Polymers49,5533
Non-polymers5913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-41 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.730, 80.340, 208.720
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: 38535.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: dinB, 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(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*G)-3')


Mass: 5508.553 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA template / Source: (synth.) Mycobacterium smegmatis (bacteria)
#3: Chemical ChemComp-2TM / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine / CMPcPP


Mass: 481.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 2KMME 12%, Bis Tris Propane pH 6.0, NaCl 0.2 mM
PH range: 6 / Temp details: 295 K

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.5→44.6 Å / Num. obs: 31909 / % possible obs: 99 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.042 / Net I/σ(I): 10.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.552 / Num. unique obs: 4401 / Rpim(I) all: 0.268 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JUL

6jul


Resolution: 2.5→44.6 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 24.074 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.587 / ESU R Free: 0.296
RfactorNum. reflection% reflectionSelection details
Rfree0.25425 1618 5.1 %RANDOM
Rwork0.20551 ---
obs0.20794 30229 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.115 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0 Å20 Å2
2---3.09 Å20 Å2
3---3.39 Å2
Refinement stepCycle: 1 / Resolution: 2.5→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5290 877 62 89 6318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0186413
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2331.8528920
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4995689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03422.877219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.96715875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9981554
X-RAY DIFFRACTIONr_chiral_restr0.1290.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214522
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.7063.4622765
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.2815.1873451
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6724.43648
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.33251.4949892
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 108 -
Rwork0.317 2097 -
obs--93.67 %
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)
13.62780.3527-0.01042.71251.53421.5168-0.043-0.09270.037-0.1557-0.00310.0648-0.10780.26620.04620.08150.021-0.04450.1746-0.07260.093612.5801-21.532223.2653
22.3347-1.2668-0.74261.83411.88052.69560.10850.0963-0.41210.12310.01490.0370.0493-0.1866-0.12340.11550.0253-0.02580.1711-0.05520.223-12.0915-21.624828.2378
30.66310.3121-0.12041.08910.33360.994-0.0598-0.0248-0.0145-0.01110.10140.0914-0.18130.092-0.04160.1673-0.0266-0.01550.1762-0.01560.0626-10.43050.611629.9769
42.09380.29881.38342.7617-1.15113.40850.01530.18080.0320.149-0.1996-0.2315-0.25030.25370.18430.2283-0.083500.11330.00960.02463.3157-4.14010.0851
53.92482.7256-0.79152.0496-0.35290.46880.0272-0.11720.114-0.00050.01340.1126-0.20590.2338-0.04060.4373-0.0524-0.0210.2118-0.03750.0536-0.4196-1.374714.7406
62.54852.18061.08852.17131.55652.0891-0.0272-0.20690.1346-0.0834-0.10940.09360.0227-0.19840.13670.1344-0.0401-0.00990.2153-0.10290.13292.133521.227246.3732
73.1476-1.7894-0.52083.29870.4420.934-0.067-0.26350.0813-0.04740.0505-0.02290.01560.07710.01640.0869-0.00220.03390.1856-0.02090.042126.735916.319450.0037
81.45210.0893-0.94242.40790.46210.8588-0.196-0.0289-0.2265-0.1664-0.15830.49140.06580.02670.35440.1555-0.0089-0.06680.1372-0.0340.240325.09433.706631.9867
92.63661.7353-0.30521.8895-0.86181.82710.12760.0017-0.0212-0.2128-0.0024-0.00890.1782-0.0717-0.12520.24570.0348-0.06380.0788-0.02330.054813.206131.994920.2107
102.7405-1.03111.47170.8105-0.22241.14210.18640.2073-0.0749-0.1976-0.00880.00290.15750.1925-0.17750.3253-0.0237-0.110.0896-0.04950.139417.303717.916725.0691
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 79
2X-RAY DIFFRACTION2A1 - 10
3X-RAY DIFFRACTION2A80 - 170
4X-RAY DIFFRACTION3A171 - 244
5X-RAY DIFFRACTION4A245 - 347
6X-RAY DIFFRACTION5B837 - 849
7X-RAY DIFFRACTION5C865 - 873
8X-RAY DIFFRACTION6F11 - 79
9X-RAY DIFFRACTION7F1 - 10
10X-RAY DIFFRACTION7F80 - 170
11X-RAY DIFFRACTION8F171 - 244
12X-RAY DIFFRACTION9F245 - 347
13X-RAY DIFFRACTION10G838 - 849
14X-RAY DIFFRACTION10H865 - 873

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