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- PDB-5yv2: DNA polymerase IV - DNA ternary complex 14 -

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Basic information

Entry
Database: PDB / ID: 5yv2
TitleDNA polymerase IV - DNA ternary complex 14
Components
  • DNA polymerase IV
  • DTN1
  • DTN2
KeywordsDNA BINDING PROTEIN / DNA POLYMERASE
Function / homology
Function and homology information


SOS response / error-free translesion synthesis / DNA synthesis involved in DNA repair / error-prone translesion synthesis / DNA-templated DNA replication / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA damage response / magnesium ion binding / cytoplasm
Similarity search - Function
: / DNA polymerase-iota, thumb domain / IMS family HHH motif / 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 ...: / DNA polymerase-iota, thumb domain / IMS family HHH motif / 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. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKottur, J. / Nair, D.T.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction
Authors: Kottur, J. / Nair, D.T.
History
DepositionNov 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: 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 / struct_conn_type
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 / _struct_conn_type.id
Revision 1.2Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: DNA polymerase IV
A: DNA polymerase IV
G: DTN1
H: DTN2
B: DTN1
C: DTN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,14113
Polymers101,7586
Non-polymers3827
Water13,043724
1
F: DNA polymerase IV
G: DTN1
H: DTN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0236
Polymers50,8793
Non-polymers1443
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-72 kcal/mol
Surface area20460 Å2
MethodPISA
2
A: DNA polymerase IV
B: DTN1
C: DTN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1187
Polymers50,8793
Non-polymers2394
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-79 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.400, 57.250, 110.950
Angle α, β, γ (deg.)90.00, 94.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules FA

#1: Protein DNA polymerase IV / Pol IV / Translesion synthesis polymerase IV / TSL polymerase IV


Mass: 39589.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: dinB, dinP, b0231, JW0221 / Production host: Escherichia coli (E. coli) / References: UniProt: Q47155, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules GBHC

#2: DNA chain DTN1


Mass: 5492.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria)
#3: DNA chain DTN2


Mass: 5796.747 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria)

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Non-polymers , 3 types, 731 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 724 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.23 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 15% MPD , pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Sep 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.9→55.28 Å / Num. obs: 85579 / % possible obs: 98.5 % / Redundancy: 4.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 12111 / CC1/2: 0.79 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ir1

4ir1


Resolution: 1.9→44.862 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 29.05
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 4292 5.09 %RANDOM
Rwork0.2037 ---
obs0.2058 84286 97.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5374 1396 19 724 7513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087050
X-RAY DIFFRACTIONf_angle_d1.0099817
X-RAY DIFFRACTIONf_dihedral_angle_d19.2354034
X-RAY DIFFRACTIONf_chiral_restr0.0571104
X-RAY DIFFRACTIONf_plane_restr0.0061031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.36782440.33435091X-RAY DIFFRACTION95
1.9216-1.94420.3492740.3234914X-RAY DIFFRACTION95
1.9442-1.96790.34682490.31925130X-RAY DIFFRACTION95
1.9679-1.99280.31092560.29425067X-RAY DIFFRACTION97
1.9928-2.0190.31873100.29285048X-RAY DIFFRACTION96
2.019-2.04670.3063000.29365037X-RAY DIFFRACTION95
2.0467-2.07590.35412650.28515135X-RAY DIFFRACTION98
2.0759-2.10690.32482590.27365130X-RAY DIFFRACTION96
2.1069-2.13980.28212760.25955060X-RAY DIFFRACTION97
2.1398-2.17490.30452910.24675124X-RAY DIFFRACTION97
2.1749-2.21240.30873170.25025152X-RAY DIFFRACTION96
2.2124-2.25270.29362640.24645097X-RAY DIFFRACTION98
2.2527-2.2960.25262360.23395145X-RAY DIFFRACTION96
2.296-2.34290.27862700.23475184X-RAY DIFFRACTION98
2.3429-2.39380.29783040.23995121X-RAY DIFFRACTION97
2.3938-2.44950.26492960.23175179X-RAY DIFFRACTION99
2.4495-2.51070.24162860.22735144X-RAY DIFFRACTION97
2.5107-2.57860.26942590.23515217X-RAY DIFFRACTION99
2.5786-2.65450.28632890.22895229X-RAY DIFFRACTION98
2.6545-2.74010.26933000.21225104X-RAY DIFFRACTION98
2.7401-2.83810.2362990.21455194X-RAY DIFFRACTION99
2.8381-2.95170.24642620.21025239X-RAY DIFFRACTION99
2.9517-3.0860.24532520.20945238X-RAY DIFFRACTION99
3.086-3.24860.25812580.19175245X-RAY DIFFRACTION99
3.2486-3.45210.20072440.17885298X-RAY DIFFRACTION99
3.4521-3.71850.19392810.1745201X-RAY DIFFRACTION99
3.7185-4.09250.23223100.16395236X-RAY DIFFRACTION99
4.0925-4.68410.21662540.15595247X-RAY DIFFRACTION100
4.6841-5.89940.23472870.17915240X-RAY DIFFRACTION99
5.8994-44.87490.18932950.17564931X-RAY DIFFRACTION94
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)
12.04230.00321.43571.7927-0.26322.5094-0.12880.28540.0501-0.33830.0097-0.76050.0940.17480.1020.2396-0.03390.09260.2473-0.01970.66764.9333-14.3467-70.4256
20.6909-0.03310.65193.10590.58521.0386-0.2260.15060.7751-0.2946-0.13180.1811-0.3349-0.18730.30510.30270.002-0.15480.2708-0.00580.73-12.40142.9943-69.7796
32.3514-0.3986-0.23331.9413-0.18641.4713-0.318-0.31410.26020.6065-0.0052-0.3472-0.1539-0.05070.28320.35010.0574-0.17860.261-0.10340.70791.4436-15.0088-44.7758
43.62890.45280.76492.9291-0.3052.228-0.2823-0.25930.7192-0.17490.16960.09430.1883-0.54490.09330.1652-0.05960.03050.4483-0.15360.2678-30.5497-19.2928-64.6244
52.8537-0.0265-0.20281.7762-0.33221.8650.0631-0.2315-0.14230.4906-0.0285-0.3150.23590.2575-0.0270.60280.0622-0.09720.38370.00470.2547-28.1216-8.58713.2611
64.0634-0.19590.33684.1863-0.70022.33560.20720.15870.32450.0463-0.1953-0.1905-0.6430.46520.00520.595-0.03410.02210.3387-0.01580.2604-25.71868.254-14.6209
72.4257-0.02211.08533.0467-1.60311.62060.06270.11070.0205-0.12690.07830.44230.0476-0.2408-0.14310.59270.00640.02570.40350.02310.2435-52.777-9.3056-4.5945
82.183-0.8724-0.15354.5486-0.41454.466-0.12440.0773-0.3540.1553-0.1576-0.22010.43470.34790.24420.4720.1570.02290.4545-0.02920.2772-27.8128-15.3401-32.5261
94.50451.5725-0.19372.9261-1.41452.1396-0.1927-0.6092-0.38120.0972-0.0774-0.17560.125-0.36490.17460.2068-0.00420.06940.354-0.06840.406-18.6173-23.9965-53.1918
102.06932.11470.86354.60651.87670.75330.1328-0.0799-0.0298-0.1054-0.28640.18970.122-0.26030.15790.67580.0256-0.01510.4848-0.04040.2846-42.6399-20.3809-24.0114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'F' and (resid 0 through 10 or resid 76 through 164 )
2X-RAY DIFFRACTION2chain 'F' and (resid 11 through 75 )
3X-RAY DIFFRACTION3chain 'F' and (resid 165 through 229 )
4X-RAY DIFFRACTION4chain 'F' and (resid 241 through 341 )
5X-RAY DIFFRACTION5chain 'A' and (resid 0 through 10 or resid 76 through 164 )
6X-RAY DIFFRACTION6chain 'A' and (resid 11 through 75 )
7X-RAY DIFFRACTION7chain 'A' and (resid 165 through 229 )
8X-RAY DIFFRACTION8chain 'A' and (resid 241 through 341 )
9X-RAY DIFFRACTION9chain 'H' and (resid 860 through 874 ) or chain 'G' and (resid 837 through 854) or chain 'F' and (resid 901 through 903)
10X-RAY DIFFRACTION10chain 'B' and (resid 837 through 854 ) or chain 'C' and (resid 857 through 874) or chain 'A' and (resid 901 through 904)

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