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- PDB-1im4: Crystal Structure of a DinB Homolog (DBH) Lesion Bypass DNA Polym... -

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Basic information

Entry
Database: PDB / ID: 1im4
TitleCrystal Structure of a DinB Homolog (DBH) Lesion Bypass DNA Polymerase Catalytic Fragment from Sulfolobus solfataricus
ComponentsDBH
KeywordsTRANSFERASE / DNA polymerase palm / thumb / fingers / helix-hairpin-helix / fidelity / processivity
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 / : / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. ...DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / : / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsPata, J.D. / Zhou, B.L. / Steitz, T.A.
Citation
Journal: Mol.Cell / Year: 2001
Title: Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain.
Authors: Zhou, B.L. / Pata, J.D. / Steitz, T.A.
#1: Journal: Mutat.Res. / Year: 1996
Title: Identification of a DinB/UmuC Homolog in the Archeon Sulfolobus solfataricus
Authors: Kulaeva, O.I. / Koonin, E.V. / McDonald, J.P. / Randall, S.K. / Rabinovich, N. / Connaughton, J.F. / Levine, A.S. / Woodgate, R.
History
DepositionMay 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: DBH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1254
Polymers24,8371
Non-polymers2883
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.988, 87.542, 76.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DBH / DBH bypass polymerase


Mass: 24836.789 Da / Num. of mol.: 1 / Fragment: N-terminal catalytic domain (residues 2-216)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: DBH / Plasmid: pNHis-DBH-216 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)pLysS / References: UniProt: P96022, DNA-directed DNA polymerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, magnesium chloride, MPD, Tris-HCl, beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
160 mg/mlprotein1drop
220 mMHEPES-NaOH1drop
350 mM1dropNaCl
45 mMbeta-mercaptoethanol1drop
50.5 mMEDTA1drop
61.5 Mammonium sulfate1reservoir
7100 mMTris-HCl1reservoir
810 mM1reservoirMgCl2
92 %(v/v)MPD1reservoir
105 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Aug 16, 2000 / Details: double crystal monochromator
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 12897 / Num. obs: 12897 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 38.4
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 3.8 / Num. unique all: 849 / % possible all: 97.8
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 97.8 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→28.91 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1260659.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0
Stereochemistry target values: Engh & Huber, as implemented in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1074 8.5 %RANDOM
Rwork0.227 ---
all0.227 12880 --
obs0.227 12634 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.12 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 52.1 Å2
Baniso -1Baniso -2Baniso -3
1-12.62 Å20 Å20 Å2
2---18.29 Å20 Å2
3---5.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 15 110 1737
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it1.482
X-RAY DIFFRACTIONc_scangle_it2.42.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.305 50 4.3 %
Rwork0.323 1110 -
obs-1164 89.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 8.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 52.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.12
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.305 / % reflection Rfree: 4.3 % / Rfactor Rwork: 0.323

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