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- PDB-1k1q: Crystal Structure of a DinB Family Error Prone DNA Polymerase fro... -

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Basic information

Entry
Database: PDB / ID: 1k1q
TitleCrystal Structure of a DinB Family Error Prone DNA Polymerase from Sulfolobus solfataricus
ComponentsDBH protein
KeywordsTRANSCRIPTION / DNA polymerase / error-prone polymerase / lesion-bypass polymerase
Function / homology
Function and homology information


DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / 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 / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family ...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 / 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
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSilvian, L.F. / Toth, E.A. / Pham, P. / Goodman, M.F. / Ellenberger, T.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus.
Authors: Silvian, L.F. / Toth, E.A. / Pham, P. / Goodman, M.F. / Ellenberger, T.
History
DepositionSep 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DBH protein
B: DBH protein


Theoretical massNumber of molelcules
Total (without water)80,0602
Polymers80,0602
Non-polymers00
Water1,22568
1
A: DBH protein


Theoretical massNumber of molelcules
Total (without water)40,0301
Polymers40,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DBH protein


Theoretical massNumber of molelcules
Total (without water)40,0301
Polymers40,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.715, 111.715, 132.175
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein DBH protein


Mass: 40029.773 Da / Num. of mol.: 2 / Mutation: C31S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: DBH / Plasmid: pET17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P96022
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG2000, sodium fluoride, magnesium chloride, cacodylate, glycerol, sucrose monolaurate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %(w/v)PEG20001drop
20.1 Msodium cacodylate1drop
30.2 M1dropNaF
45 mM1dropMgCl2
50.2 mMsucrose monolaurate1drop
610 %(v/v)PEG20001reservoir
750 mMsodium cacodylate1reservoir
80.1 M1reservoirNaF
95 mM1reservoirMgCl2
1040 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jul 23, 2001
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→43 Å / Num. all: 22972 / Num. obs: 21610 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.6
Reflection shellResolution: 2.8→2.98 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2260 / % possible all: 71.3
Reflection
*PLUS
Lowest resolution: 43 Å
Reflection shell
*PLUS
% possible obs: 71.3 %

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Processing

Software
NameVersionClassification
EPMRphasing
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→40.1 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1550344.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.306 2141 9.9 %RANDOM
Rwork0.263 ---
all-22972 --
obs-21569 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.3907 Å2 / ksol: 0.380826 e/Å3
Displacement parametersBiso mean: 72.3 Å2
Baniso -1Baniso -2Baniso -3
1-11.125 Å2-12.448 Å20 Å2
2--11.125 Å20 Å2
3----22.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.8→40.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5098 0 0 68 5166
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009991
X-RAY DIFFRACTIONc_angle_deg1.78836
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d1.23
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.41 321 10.8 %
Rwork0.392 2651 -
obs--77.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 72.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.34
LS refinement shell
*PLUS
Rfactor Rfree: 0.41 / % reflection Rfree: 10.8 % / Rfactor Rwork: 0.392

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