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- PDB-6jul: MsDpo4-DNA complex 1 -

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Basic information

Entry
Database: PDB / ID: 6jul
TitleMsDpo4-DNA complex 1
Components
  • DNA (5'-D(P*CP*CP*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


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 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-0KX / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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.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
F: DNA polymerase IV
H: DNA (5'-D(P*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
G: DNA (5'-D(P*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
A: DNA polymerase IV
C: DNA (5'-D(P*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
B: DNA (5'-D(P*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,88612
Polymers99,8566
Non-polymers1,0306
Water5,116284
1
F: DNA polymerase IV
H: DNA (5'-D(P*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
G: DNA (5'-D(P*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4436
Polymers49,9283
Non-polymers5153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-51 kcal/mol
Surface area18830 Å2
MethodPISA
2
A: DNA polymerase IV
C: DNA (5'-D(P*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
B: DNA (5'-D(P*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4436
Polymers49,9283
Non-polymers5153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-46 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.960, 80.780, 210.520
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: 38910.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Gene: dinB, MSMEG_1014, MSMEG_2294 / Variant: ATCC 700084 / mc(2)155 / Production host: Escherichia coli (E. coli) / Variant (production host): C41DE3 / References: UniProt: A0QR77, DNA-directed DNA polymerase
#2: DNA chain
DNA (5'-D(P*CP*CP*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.) Escherichia coli (E. coli)
#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.: 284 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 15% PEG 2KMME, 0.2M NaCl, Bis Tris Propane pH 6.0, / PH range: 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953724 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953724 Å / Relative weight: 1
ReflectionResolution: 2.3→70.173 Å / Num. obs: 41973 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.063 / Net I/σ(I): 10.2
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6034 / CC1/2: 0.629 / Rpim(I) all: 0.413 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHENIXrefinement
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→70.173 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.901 / SU B: 16.72 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.245
RfactorNum. reflection% reflectionSelection details
Rfree0.25934 2145 5.1 %RANDOM
Rwork0.2004 ---
obs0.20332 39754 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.205 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å2-0 Å2
2--0.87 Å20 Å2
3----0.15 Å2
Refinement stepCycle: 1 / Resolution: 2.3→70.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5290 838 60 284 6472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0186410
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.381.8668879
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0645692
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89422.909220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.42415830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7931554
X-RAY DIFFRACTIONr_chiral_restr0.1460.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214520
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_it1.8682.4072774
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9723.6013464
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2193.1533636
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.70336.1899821
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 175 -
Rwork0.275 2897 -
obs--100 %
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)
11.860.09180.37190.20520.10061.724-0.0265-0.04990.0479-0.047-0.0210.0053-0.05330.11480.04750.01380.0115-0.00310.0479-0.01850.1409-13.9009-61.673523.2855
21.0292-0.51260.0020.90380.75311.73730.06180.061-0.2899-0.0285-0.01670.10370.006-0.1185-0.04510.0076-0.0016-0.01120.0338-0.0050.2101-38.5893-61.61828.5402
30.51910.55750.13961.65040.8650.5292-0.0186-0.0638-0.05850.06250.00970.01610.04910.04020.00890.0358-0.0004-0.00380.0679-0.00030.1107-37.228-39.359530.2172
41.7448-0.23751.02581.0658-1.19591.72270.01350.22160.09650.0775-0.1835-0.0966-0.06530.23880.170.0239-0.0321-0.02710.11260.01580.0809-22.9892-44.81-0.1975
50.70760.9799-0.05231.3903-0.05940.39970.01070.00250.07920.0882-0.05110.1815-0.30720.05520.04030.2599-0.0057-0.06180.06950.00390.1781-27.7412-40.798613.5804
61.62220.31280.63780.158-0.03360.5055-0.0393-0.20940.0601-0.06460.01050.01510.0635-0.16310.02880.04360.0029-0.00490.103-0.05190.1178-24.4952-18.705846.598
70.6131-0.4109-0.45132.61440.13210.9205-0.0467-0.20770.0652-0.18060.033-0.1488-0.06660.22470.01370.04450.011-0.0030.1484-0.04080.09110.1834-23.542750.4768
80.7066-0.0561-0.25941.1255-0.26530.664-0.00470.0681-0.1216-0.1297-0.03080.26950.01740.00740.03550.01660.0051-0.0260.0367-0.01640.161-1.6378-36.35332.5276
90.98471.2014-0.66781.7388-0.52082.2118-0.03140.12460.0156-0.09220.08480.01570.12510.002-0.05340.06530.0263-0.00090.04770.00110.0804-13.4377-8.011720.1702
101.4643-0.55751.10440.6818-0.09681.06810.09530.0708-0.0364-0.17690.0615-0.02810.03890.157-0.15690.0861-0.037-0.00580.0519-0.03160.1695-10.2043-22.248526.9812
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 DIFFRACTION5B838 - 849
7X-RAY DIFFRACTION5C864 - 873
8X-RAY DIFFRACTION6F11 - 79
9X-RAY DIFFRACTION7F1 - 10
10X-RAY DIFFRACTION7F80 - 170
11X-RAY DIFFRACTION8F171 - 244
12X-RAY DIFFRACTION9F245 - 347
13X-RAY DIFFRACTION10G838 - 848
14X-RAY DIFFRACTION10H866 - 873

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