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- PDB-4q44: Polymerase-Damaged DNA Complex -

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Basic information

Entry
Database: PDB / ID: 4q44
TitlePolymerase-Damaged DNA Complex
Components
  • DNA (5'-D(*TP*CP*TP*AP*(RDG)P*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / POLYMERASE / DNA POLYMERASE / DNA / TRANSFERASE-DNA COMPLEX
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
Chem-1FZ / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsNair, D.T. / Kottur, J. / Sharma, A.
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_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.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*AP*(RDG)P*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
C: DNA (5'-D(*TP*CP*TP*AP*(RDG)P*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
G: DNA (5'-D(*TP*CP*TP*AP*(RDG)P*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
H: DNA (5'-D(*TP*CP*TP*AP*(RDG)P*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,95912
Polymers98,8996
Non-polymers1,0606
Water1,56787
1
A: DNA polymerase IV
B: DNA (5'-D(*TP*CP*TP*AP*(RDG)P*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
C: DNA (5'-D(*TP*CP*TP*AP*(RDG)P*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9796
Polymers49,4503
Non-polymers5303
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-48 kcal/mol
Surface area21520 Å2
MethodPISA
2
F: DNA polymerase IV
G: DNA (5'-D(*TP*CP*TP*AP*(RDG)P*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
H: DNA (5'-D(*TP*CP*TP*AP*(RDG)P*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9796
Polymers49,4503
Non-polymers5303
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-50 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.655, 56.934, 110.396
Angle α, β, γ (deg.)90.00, 94.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA polymerase IV / Pol IV


Mass: 38304.277 Da / Num. of mol.: 2 / Fragment: UNP Residues 2-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0231 / Plasmid: PGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3 / References: UniProt: Q47155, DNA-directed DNA polymerase
#2: DNA chain
DNA (5'-D(*TP*CP*TP*AP*(RDG)P*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')


Mass: 5572.639 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically Synthesized DNA Oligonucleotide / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-1FZ / 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine


Mass: 481.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N3O13P3
#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.: 87 / 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: 2.74 Å3/Da / Density % sol: 55.18 %
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: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 29593 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.9
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 2.2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IR1

4ir1


Resolution: 2.71→48.21 Å / SU ML: 0.33 / σ(F): 1.36 / Phase error: 29.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27 1501 5.07 %
Rwork0.225 --
obs0.227 29593 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.53 Å2 / Biso mean: 62.4 Å2 / Biso min: 35.09 Å2
Refinement stepCycle: LAST / Resolution: 2.71→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5372 1383 62 87 6904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037082
X-RAY DIFFRACTIONf_angle_d0.8459865
X-RAY DIFFRACTIONf_dihedral_angle_d21.0152759
X-RAY DIFFRACTIONf_chiral_restr0.0571103
X-RAY DIFFRACTIONf_plane_restr0.0041037
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7052-2.79250.33361000.31562489258998
2.7925-2.89230.3881380.31142538267699
2.8923-3.00810.35511310.296725292660100
3.0081-3.1450.33491510.281225332684100
3.145-3.31070.33351430.261625252668100
3.3107-3.51810.31781200.241225452665100
3.5181-3.78960.29951500.225325672717100
3.7896-4.17080.24351250.207825722697100
4.1708-4.77390.22561380.188825862724100
4.7739-6.01270.21581430.2125692712100
6.0127-48.21710.21271620.17562639280199

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