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- PDB-4irk: structure of Polymerase-DNA complex, dna -

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Basic information

Entry
Database: PDB / ID: 4irk
Titlestructure of Polymerase-DNA complex, dna
Components
  • DNA (5'-D(*CP*TP*A*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3')
  • DNA (5'-D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
  • DNA polymerase IV
KeywordsTransferase/DNA / DNA Polymerase / Y-family / Transferase-DNA complex
Function / homology
Function and homology information


DNA synthesis involved in DNA repair / error-free translesion synthesis / SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA damage response / magnesium ion binding / cytoplasm
Similarity search - Function
DNA polymerase type-Y, HhH motif / 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 ...DNA polymerase type-Y, HhH motif / 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsNair, D.T. / Sharma, A.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli.
Authors: Sharma, A. / Kottur, J. / Narayanan, N. / Nair, D.T.
History
DepositionJan 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Other
Revision 1.2May 29, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_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.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_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA polymerase IV
C: DNA (5'-D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
G: DNA (5'-D(*CP*TP*A*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3')
A: DNA polymerase IV
F: DNA (5'-D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
H: DNA (5'-D(*CP*TP*A*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,92110
Polymers97,9386
Non-polymers9834
Water5,837324
1
B: DNA polymerase IV
C: DNA (5'-D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
G: DNA (5'-D(*CP*TP*A*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4615
Polymers48,9693
Non-polymers4912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-46 kcal/mol
Surface area20550 Å2
MethodPISA
2
A: DNA polymerase IV
F: DNA (5'-D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
H: DNA (5'-D(*CP*TP*A*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4615
Polymers48,9693
Non-polymers4912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-41 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.650, 57.080, 110.230
Angle α, β, γ (deg.)90.00, 94.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein DNA polymerase IV / / Pol IV


Mass: 38304.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: k12 / Gene: b0231, dinB, dinP, JW0221 / Production host: Escherichia coli (E. coli) / Strain (production host): c41de3 / References: UniProt: Q47155, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules CFGH

#2: DNA chain DNA (5'-D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')


Mass: 5492.554 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*TP*A*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3')


Mass: 5172.362 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 3 types, 328 molecules

#4: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate


Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 15% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. all: 44132 / Num. obs: 44132 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 8.4
Reflection shellResolution: 2.32→2.45 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.7 / % possible all: 99.2

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Processing

Software
NameVersionClassification
RSDQdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→35.18 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / SU B: 14.783 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26236 2358 5.1 %RANDOM
Rwork0.20876 ---
obs0.21137 44132 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.704 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å2-0.65 Å2
2---1.64 Å2-0 Å2
3---1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.32→35.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5376 1294 58 324 7052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0186986
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.7959722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2675682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25822.439246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3815982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.841562
X-RAY DIFFRACTIONr_chiral_restr0.1150.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214806
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 187 -
Rwork0.282 3229 -
obs--99.01 %
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)
12.3522-0.1269-0.11370.95450.411.1806-0.0050.0851-0.1006-0.17390.00560.10060.002-0.1355-0.00050.1788-0.0691-0.01030.16390.00520.01733.308319.3972-58.6327
20.9079-0.14310.22491.34440.41872.06080.01210.03230.14210.06420.00430.0678-0.2102-0.1855-0.01640.19310.02720.05250.11880.03820.045730.458935.796-40.681
30.5387-0.12830.3263.07540.21822.59150.06350.02810.04540.07220.0492-0.11890.00180.2988-0.11270.14620.00240.04650.1873-0.04110.032557.429118.1903-49.8275
40.75840.1870.41251.65860.55222.9288-0.0667-0.05060.0009-0.0694-0.0181-0.02570.1833-0.17660.08490.1345-0.07870.05920.180.00160.040632.516712.1608-22.6363
50.57070.58640.58171.6358-0.20881.69520.0627-0.04770.00850.1989-0.0520.35730.0192-0.0392-0.01070.03530.00610.08440.11310.03070.2636-0.778313.507914.84
61.97521.8927-0.31812.0101-0.28840.64710.2281-0.22660.25610.2583-0.35830.0525-0.05340.14820.13020.1092-0.0284-0.05830.17620.11660.321216.935930.265214.5881
72.36920.1148-0.80842.5520.19531.3964-0.15870.0025-0.0148-0.33290.03780.1626-0.00330.05090.1210.1022-0.0342-0.03260.09890.03060.19773.651512.4978-10.4039
82.2820.1320.07181.2784-0.49781.7494-0.18590.21210.22560.20390.0277-0.03020.18840.29530.15820.10630.05040.02110.21830.11570.14335.06198.29959.2778
90.5168-0.6430.44260.9361-0.40110.76130.08840.13420.02390.0208-0.16490.01640.11440.19650.07650.20940.03170.04260.16670.00510.032546.5968.4057-31.2785
101.8593-0.15410.31160.89860.65720.58220.02760.1947-0.09640.0103-0.09980.0940.0136-0.01810.07220.1005-0.00210.08570.16130.06250.170923.7832.8047-3.1212
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 10
2X-RAY DIFFRACTION1B77 - 166
3X-RAY DIFFRACTION2B11 - 76
4X-RAY DIFFRACTION3B167 - 231
5X-RAY DIFFRACTION4B241 - 341
6X-RAY DIFFRACTION5A1 - 10
7X-RAY DIFFRACTION5A77 - 166
8X-RAY DIFFRACTION6A11 - 76
9X-RAY DIFFRACTION7A167 - 231
10X-RAY DIFFRACTION8A241 - 341
11X-RAY DIFFRACTION9C837 - 854
12X-RAY DIFFRACTION9G860 - 872
13X-RAY DIFFRACTION9G873
14X-RAY DIFFRACTION9B402
15X-RAY DIFFRACTION10F837 - 854
16X-RAY DIFFRACTION10A401
17X-RAY DIFFRACTION10A402

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