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- PDB-6jum: MsDpo4-DNA complex 2 -

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Basic information

Entry
Database: PDB / ID: 6jum
TitleMsDpo4-DNA complex 2
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsNair, D.T. / Johnson, M.J.
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 1.1Feb 26, 2020Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.2Nov 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.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
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')
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)98,42712
Polymers97,3986
Non-polymers1,0306
Water12,502694
1
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)49,2146
Polymers48,6993
Non-polymers5153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-46 kcal/mol
Surface area19580 Å2
MethodPISA
2
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)49,2146
Polymers48,6993
Non-polymers5153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-48 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.020, 80.960, 211.610
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: 37681.809 Da / Num. of mol.: 2 / Mutation: C47T
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*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: isolated from a genetically manipulated source
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.: 694 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 2KMME 12%, NaCl 0.2 mM, 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: ID30B / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.78→105.81 Å / Num. obs: 89850 / % possible obs: 99.8 % / Redundancy: 9.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Net I/σ(I): 10.9
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 10 % / Num. unique obs: 12978 / CC1/2: 0.53 / % possible all: 99.7

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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: 1.78→80.96 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.245 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.121
RfactorNum. reflection% reflectionSelection details
Rfree0.23377 4626 5.2 %RANDOM
Rwork0.19524 ---
obs0.19724 85085 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0 Å20 Å2
2--0.26 Å2-0 Å2
3---0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.78→80.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5292 882 60 694 6928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0186430
X-RAY DIFFRACTIONr_bond_other_d0.0020.025723
X-RAY DIFFRACTIONr_angle_refined_deg2.2451.8518947
X-RAY DIFFRACTIONr_angle_other_deg1.26313192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345692
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.36122.811217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05215875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9671554
X-RAY DIFFRACTIONr_chiral_restr0.1630.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0216580
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021376
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_it1.5721.4062774
X-RAY DIFFRACTIONr_mcbond_other1.5721.4042773
X-RAY DIFFRACTIONr_mcangle_it2.5492.0963464
X-RAY DIFFRACTIONr_mcangle_other2.5492.0993465
X-RAY DIFFRACTIONr_scbond_it2.4722.1443656
X-RAY DIFFRACTIONr_scbond_other2.4712.1443655
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8023.1325484
X-RAY DIFFRACTIONr_long_range_B_refined7.16821.4467596
X-RAY DIFFRACTIONr_long_range_B_other7.02820.317373
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 352 -
Rwork0.281 6180 -
obs--99.6 %
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)
10.54890.69640.32821.04850.22290.6943-0.02270.0223-0.0501-0.0037-0.02090.0214-0.04580.0560.04360.12820.01-0.01450.162-0.02280.1672-14.0297-61.481723.0297
21.4335-0.066-0.40120.04620.12080.37390.01060.0782-0.2865-0.0181-0.0118-0.0261-0.0914-0.02420.00110.1260.0116-0.01720.1744-0.01150.2161-38.8312-61.602128.429
30.23660.1206-0.12060.48320.11810.14120.0037-0.0097-0.0349-0.0325-0.0001-0.0096-0.0250.0125-0.00360.188-0.00850.00220.17830.00660.1384-37.1837-38.997830.5408
40.89440.21470.61230.7059-0.73251.6587-0.04190.12820.01750.0623-0.0801-0.026-0.12980.18860.1220.1805-0.0442-0.03230.23040.01960.1152-23.0539-44.7869-0.3429
51.05541.3762-0.50961.8034-0.66390.24820.1354-0.02690.0650.2246-0.07570.1088-0.08420.0327-0.05970.29340.0645-0.06330.2483-0.0350.1008-28.2293-39.924213.0504
60.87670.57660.5720.39240.32530.8262-0.0726-0.07780.0636-0.0815-0.00330.01580.0925-0.09970.07590.1419-0.0220.00940.2123-0.06760.1289-24.5148-18.705146.7115
70.6164-0.4635-0.22410.42810.12430.3246-0.0358-0.16410.0291-0.06150.0605-0.04680.00510.0893-0.02460.14250.01220.00910.235-0.04370.13650.2963-23.633150.9433
80.225-0.05290.07280.29310.21420.21970.0083-0.0087-0.0733-0.0677-0.01660.0729-0.0580.01570.00830.16780.011-0.0140.1843-0.02150.1684-1.8602-36.535532.6874
91.18460.38540.32450.5326-0.45550.9948-0.02570.03690.0198-0.0790.01570.01320.06740.01160.00990.1853-0.00680.00540.1376-0.00470.1125-13.5262-8.040920.2971
100.6216-0.1451-0.03710.0360.01210.01760.0624-0.02320.0866-0.00130.003-0.02730.02030.0036-0.06540.20780.0012-0.0280.13350.00510.1728-9.7964-22.38726.3061
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 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 - 849
14X-RAY DIFFRACTION10H866 - 873

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