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- PDB-7yll: Crystal structure of TTEDbh -

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Basic information

Entry
Database: PDB / ID: 7yll
TitleCrystal structure of TTEDbh
ComponentsDNA polymerase IV
KeywordsTRANSFERASE / polymerase of DinB subfamily / translesion synthesis / DNA binding protein / REPLICATION
Function / homology
Function and homology information


SOS response / 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 / 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/RNA polymerase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / DNA polymerase IV
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.60000921196 Å
AuthorsYan, X. / Tian, L. / Gao, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Structure and function of extreme TLS DNA polymerase TTEDbh from Thermoanaerobacter tengcongensis.
Authors: Tian, L.F. / Gao, H. / Yang, S. / Liu, Y.P. / Li, M. / Xu, W. / Yan, X.X.
History
DepositionJul 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1083
Polymers43,9881
Non-polymers1192
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-17 kcal/mol
Surface area17420 Å2
Unit cell
Length a, b, c (Å)105.196, 105.196, 74.211
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-532-

HOH

21A-646-

HOH

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Components

#1: Protein DNA polymerase IV / Pol IV


Mass: 43988.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: dinB, TTE0254 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P58965, DNA-directed DNA polymerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 500 mM NaCl, 5 mM Mg3(PO4)2, 18% [w/v] PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97929 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.6→14.88 Å / Num. obs: 22314 / % possible obs: 98.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 46.7017201672 Å2 / CC1/2: 0.98 / Net I/σ(I): 133.9
Reflection shellResolution: 2.6→2.77 Å / Num. unique obs: 2185 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.12-2829_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RDI

2rdi


Resolution: 2.60000921196→14.8769609907 Å / SU ML: 0.310977302148 / Cross valid method: FREE R-VALUE / σ(F): 1.33649243903 / Phase error: 26.6724387516
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.265306133501 662 5.00832198517 %
Rwork0.229796337959 12556 -
obs0.231538208837 13218 99.9395130803 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.012083344 Å2
Refinement stepCycle: LAST / Resolution: 2.60000921196→14.8769609907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2589 0 6 162 2757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008206622205972637
X-RAY DIFFRACTIONf_angle_d1.396558012973561
X-RAY DIFFRACTIONf_chiral_restr0.0807025188084415
X-RAY DIFFRACTIONf_plane_restr0.00867601648747447
X-RAY DIFFRACTIONf_dihedral_angle_d24.91034268611003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.601-2.79950.357084946061460.2693100402722447X-RAY DIFFRACTION100
2.7995-3.0790.3736144207831220.2831768551542465X-RAY DIFFRACTION99.9613601236
3.079-3.51940.3129363807181220.2507999489682493X-RAY DIFFRACTION99.9617737003
3.5194-4.41480.2217089795151270.210841131172518X-RAY DIFFRACTION99.9622071051
4.4148-14.87690.2214883373791450.208236566562633X-RAY DIFFRACTION99.820337765

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