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- PDB-6juo: MsDpo4-DNA complex 4 -

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Basic information

Entry
Database: PDB / ID: 6juo
TitleMsDpo4-DNA complex 4
Components
  • DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*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-0KX / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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 / 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
A: DNA polymerase IV
B: DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*G)-3')
C: DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*G)-3')
F: DNA polymerase IV
G: DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*G)-3')
H: DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,23512
Polymers99,2066
Non-polymers1,0306
Water7,602422
1
A: DNA polymerase IV
B: DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*G)-3')
C: DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1186
Polymers49,6033
Non-polymers5153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-49 kcal/mol
Surface area20190 Å2
MethodPISA
2
F: DNA polymerase IV
G: DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*G)-3')
H: DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1186
Polymers49,6033
Non-polymers5153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-48 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.100, 81.030, 210.530
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: 38585.828 Da / Num. of mol.: 2 / Mutation: L14Y
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) / Variant (production host): C41DE3 / References: UniProt: A0QR77, DNA-directed DNA polymerase
#2: DNA chain
DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*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-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 / Feature type: SUBJECT OF INVESTIGATION
#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.: 422 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 2KMME 12%, 0.2mM NaCl, Bis Tris Propane 6.0 / PH range: 6

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 K / 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: 2.16→70.177 Å / Num. obs: 50583 / % possible obs: 100 % / Redundancy: 8.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.039 / Net I/σ(I): 12.4
Reflection shellResolution: 2.16→2.28 Å / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 7237 / CC1/2: 0.884 / Rpim(I) all: 0.199 / % possible all: 100

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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: 2.16→70.177 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.909 / SU B: 11.927 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.21 / Details: HYDROGENS WERE NOT ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25513 2560 5.1 %RANDOM
Rwork0.20025 ---
obs0.20301 47928 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.932 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å2-0 Å20 Å2
2--0.86 Å2-0 Å2
3---0.63 Å2
Refinement stepCycle: 1 / Resolution: 2.16→70.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 902 60 422 6682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0186477
X-RAY DIFFRACTIONr_bond_other_d0.0030.025735
X-RAY DIFFRACTIONr_angle_refined_deg2.1871.8569013
X-RAY DIFFRACTIONr_angle_other_deg1.246313228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4555694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58822.883222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33415836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1421554
X-RAY DIFFRACTIONr_chiral_restr0.130.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216636
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021388
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_it2.2852.6952779
X-RAY DIFFRACTIONr_mcbond_other2.2782.6932778
X-RAY DIFFRACTIONr_mcangle_it3.474.0283472
X-RAY DIFFRACTIONr_mcangle_other3.474.0313473
X-RAY DIFFRACTIONr_scbond_it3.3243.7023698
X-RAY DIFFRACTIONr_scbond_other3.3243.7023697
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.065.4395541
X-RAY DIFFRACTIONr_long_range_B_refined7.34436.4637616
X-RAY DIFFRACTIONr_long_range_B_other7.29236.0757514
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.162→2.218 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 189 -
Rwork0.276 3463 -
obs--99.81 %
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)
10.6191-0.45790.45580.9765-0.18530.968-0.0530.0245-0.08470.0856-0.0516-0.0217-0.0577-0.09630.10460.0818-0.0112-0.02070.11630.03220.1247-12.9957-21.3094-23.0642
21.64780.3762-0.5150.1047-0.18880.6094-0.0255-0.0962-0.3264-0.0228-0.0169-0.061-0.03760.04190.04250.08340.0007-0.01440.08650.03160.187411.864-21.3155-28.5146
30.2104-0.0591-0.04860.4338-0.31660.45570.00380.004-0.04870.04220.0662-0.0159-0.1183-0.0714-0.070.15530.02910.01110.09030.02340.088310.16511.3167-30.3233
41.2645-0.01920.71650.46550.68791.5022-0.0311-0.15620.0585-0.0966-0.12920.0522-0.1563-0.25730.16030.17530.0583-0.04440.141-0.0080.06-3.7272-4.59910.2964
50.1133-0.22430.04480.4652-0.10690.0706-0.00040.02830.0340.0273-0.0675-0.1093-0.1155-0.02420.0680.32210.0376-0.1160.12820.02470.10722.47681.4133-12.4712
60.988-0.8370.86581.0338-0.36251.2573-0.12440.1180.14450.19780.0376-0.0927-0.01870.17240.08680.08540.01310.00120.15320.10630.1369-2.48221.7848-46.468
70.95010.4167-0.45761.543-0.29040.2296-0.07380.23880.05210.06750.0811-0.00730.0301-0.0982-0.00720.0587-0.00750.02370.15340.07250.1002-27.297216.9429-50.4143
80.11930.14810.07630.7847-0.35160.3865-0.0054-0.0388-0.06930.0858-0.0353-0.2309-0.0552-0.05920.04070.1144-0.0018-0.0290.08270.04310.1545-25.15093.8611-32.2813
91.6617-0.51190.45990.50.42861.07810.0447-0.02760.05840.1042-0.0112-0.04670.2076-0.0482-0.03350.21610.0196-0.00550.0290.0070.0285-13.561332.5904-20.1219
101.43530.27190.98970.05360.18780.68520.1222-0.0427-0.05660.0509-0.0329-0.01390.1051-0.0354-0.08940.24960.0753-0.010.04050.03990.1342-16.703718.2668-26.7457
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 - 850
7X-RAY DIFFRACTION5C862 - 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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