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- PDB-4q43: Polymerase-damaged DNA complex -

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Basic information

Entry
Database: PDB / ID: 4q43
TitlePolymerase-damaged DNA complex
Components
  • DNA (5'-D(*T*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
  • DNA (5'-D(*TP*CP*TP*(RDG)P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / POLYMERASE / DNA POLYMERASE / TRANSLESION SYNTHESIS / 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
Chem-0KX / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKottur, J. / Sharma, A. / Nair, D.T.
CitationJournal: Structure / Year: 2015
Title: Unique structural features in DNA polymerase IV enable efficient bypass of the N2 adduct induced by the nitrofurazone antibiotic
Authors: Kottur, J. / Sharma, A. / Gore, K.R. / Narayanan, N. / Samanta, B. / Pradeepkumar, P.I. / Nair, D.T.
History
DepositionApr 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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_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_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
A: DNA polymerase IV
F: DNA polymerase IV
B: DNA (5'-D(*TP*CP*TP*(RDG)P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
C: DNA (5'-D(*T*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
G: DNA (5'-D(*TP*CP*TP*(RDG)P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
H: DNA (5'-D(*T*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,37212
Polymers101,3426
Non-polymers1,0306
Water2,180121
1
A: DNA polymerase IV
B: DNA (5'-D(*TP*CP*TP*(RDG)P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
C: DNA (5'-D(*T*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1866
Polymers50,6713
Non-polymers5153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-53 kcal/mol
Surface area21470 Å2
MethodPISA
2
F: DNA polymerase IV
G: DNA (5'-D(*TP*CP*TP*(RDG)P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
H: DNA (5'-D(*T*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1866
Polymers50,6713
Non-polymers5153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-52 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.830, 56.790, 112.020
Angle α, β, γ (deg.)90.00, 91.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AF

#1: Protein DNA polymerase IV / / Pol IV


Mass: 39589.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dinB / Plasmid: PGEX6P1 / 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 BGCH

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


Mass: 5588.638 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized DNA oligonucleotide / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*T*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 / Details: Chemically synthesized DNA oligonucleotide / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 127 molecules

#4: 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
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M ACETATE, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 39632 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.7
Reflection shellResolution: 2.42→2.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IRC

4irc


Resolution: 2.45→40.52 Å / SU ML: 0.28 / σ(F): 0.73 / Phase error: 30.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 1985 4.99 %
Rwork0.214 --
obs0.217 39632 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.23 Å2 / Biso mean: 53.36 Å2 / Biso min: 15.65 Å2
Refinement stepCycle: LAST / Resolution: 2.45→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5370 1370 60 121 6921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077065
X-RAY DIFFRACTIONf_angle_d1.2169843
X-RAY DIFFRACTIONf_dihedral_angle_d21.7622762
X-RAY DIFFRACTIONf_chiral_restr0.0731102
X-RAY DIFFRACTIONf_plane_restr0.0051037
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.48220.38361110.31072690280196
2.4822-2.51620.31681320.29712761289397
2.5162-2.55220.35021290.2752726285596
2.5522-2.59030.3321540.29462757291196
2.5903-2.63070.30611390.27842737287697
2.6307-2.67390.32141580.28042710286896
2.6739-2.720.36881570.27542754291196
2.72-2.76940.26071370.25822709284696
2.7694-2.82270.31271530.26382628278194
2.8227-2.88030.36511420.26962629277192
2.8803-2.94290.39551120.26762598271091
2.9429-3.01130.36121470.26852665281293
3.0113-3.08660.2491440.24982722286697
3.0866-3.170.31481250.23622781290697
3.17-3.26320.32571420.22312735287798
3.2632-3.36850.26121460.20542781292797
3.3685-3.48890.27551440.21332786293097
3.4889-3.62850.29621650.20832698286397
3.6285-3.79350.21421740.20952735290995
3.7935-3.99330.26871230.19552683280694
3.9933-4.24330.2081370.18182590272792
4.2433-4.57050.23621660.18062621278793
4.5705-5.02970.24931400.18762491263188
5.0297-5.75570.23951210.22283240480
5.7557-7.24480.26241160.21152470258687
7.2448-40.52250.21211220.15292468259087

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