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- PDB-2rdi: Snapshots of a Y-family DNA polymerase in replication: Dpo4 in ap... -

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Basic information

Entry
Database: PDB / ID: 2rdi
TitleSnapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms
ComponentsDNA polymerase IV
KeywordsTRANSFERASE / DNA polymerase / apo-enzyme / Y-family / DNA damage / DNA repair / DNA replication / DNA-binding / DNA-directed DNA polymerase / Magnesium / Metal-binding / Mutator protein / Nucleotidyltransferase
Function / homology
Function and homology information


error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / 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 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
DI(HYDROXYETHYL)ETHER / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / Resolution: 1.92 Å
AuthorsWong, J.H.Y. / Ling, H.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Snapshots of a Y-family DNA polymerase in replication: substrate-induced conformational transitions and implications for fidelity of Dpo4.
Authors: Wong, J.H. / Fiala, K.A. / Suo, Z. / Ling, H.
History
DepositionSep 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / 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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3193
Polymers39,1211
Non-polymers1982
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.927, 51.069, 86.026
Angle α, β, γ (deg.)90.000, 98.080, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA polymerase IV / Pol IV


Mass: 39120.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: dbh, dpo4 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97W02, DNA-directed DNA polymerase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 20% PEG3350, 0.2M lithium nitrate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 4, 2005
RadiationMonochromator: GRADED MULTILAYER (OSMIC) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. all: 30796 / Num. obs: 28887 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3 % / Biso Wilson estimate: 37.479 Å2 / Rmerge(I) obs: 0.043 / Χ2: 1.031 / Net I/σ(I): 16.8
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.507 / Num. unique all: 1393 / Χ2: 1.125 / % possible all: 90.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
PHASERphasing
RefinementStarting model: PDB ENTRY 1JX4

1jx4


Resolution: 1.92→20.35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.54 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -1 / ESU R: 0.171 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1217 4.2 %RANDOM
Rwork0.205 ---
all0.207 29312 --
obs0.207 27934 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.92→20.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2701 0 13 235 2949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222769
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9953719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64523.782119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55415560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3661523
X-RAY DIFFRACTIONr_chiral_restr0.1040.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021992
X-RAY DIFFRACTIONr_nbd_refined0.2080.21334
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21922
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2198
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.214
X-RAY DIFFRACTIONr_mcbond_it0.7381.51752
X-RAY DIFFRACTIONr_mcangle_it1.11622743
X-RAY DIFFRACTIONr_scbond_it1.84931146
X-RAY DIFFRACTIONr_scangle_it2.8154.5974
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 81 -
Rwork0.329 1989 -
all-2070 -
obs--100 %

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