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- PDB-1jxl: Crystal Structure of a Y-Family DNA Polymerase in a Ternary Compl... -

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Basic information

Entry
Database: PDB / ID: 1jxl
TitleCrystal Structure of a Y-Family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide
Components
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*T)-3'
  • 5'-D(*T*TP*CP*GP*AP*AP*(BRU)P*CP*CP*TP*(BRU)P*CP*CP*CP*CP*C)-3'
  • DNA polymerase IV (family Y)
KeywordsTRANSFERASE/DNA / DNA polymerase / protein-DNA complex / Y-family / TRANSFERASE-DNA COMPLEX
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
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsLing, H. / Boudsocq, F. / Woodgate, R. / Yang, W.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication.
Authors: Ling, H. / Boudsocq, F. / Woodgate, R. / Yang, W.
History
DepositionSep 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 1.4Aug 16, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_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
P: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*T)-3'
T: 5'-D(*T*TP*CP*GP*AP*AP*(BRU)P*CP*CP*TP*(BRU)P*CP*CP*CP*CP*C)-3'
A: DNA polymerase IV (family Y)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6069
Polymers48,9403
Non-polymers6666
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.120, 101.880, 52.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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DNA chain , 2 types, 2 molecules PT

#1: DNA chain 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*T)-3'


Mass: 3807.489 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*T*TP*CP*GP*AP*AP*(BRU)P*CP*CP*TP*(BRU)P*CP*CP*CP*CP*C)-3'


Mass: 4874.819 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#3: Protein DNA polymerase IV (family Y)


Mass: 40257.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: dpo4 / Plasmid: pet22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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Non-polymers , 5 types, 258 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16% PEG 3350, 0.1M Hepes (pH7.0), 100 mM calcium acetate, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2Hepes(pH7.0)11
3calcium acetate11
4glycerol11
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMddATP1dropor ddGTP
220 mMHEPES1drop
360 mM1dropNaCl
45 mM1dropMgCl2
51.0 mMdithiothreitol1drop
68 mg/mlprotein1drop
716 %PEG33501reservoir
80.1 MHEPES1reservoir
9100 mMcalcium acetate1reservoir
102.5 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9824 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 1, 2001 / Details: mirrors
RadiationMonochromator: Si crystals / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9824 Å / Relative weight: 1
ReflectionResolution: 2.1→500 Å / Num. all: 31140 / Num. obs: 30292 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.1 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 24.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1490 / Rsym value: 0.331 / % possible all: 98.1
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1JX4

1jx4


Resolution: 2.1→500 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1452 -identical to the corresponding data randomly selected in 1JX4 and randomly selected in the data pool which does not exist in 1JX4 dataset
Rwork0.221 ---
all0.278 31140 --
obs0.278 30292 97.3 %-
Displacement parametersBiso mean: 41.7 Å2
Baniso -1Baniso -2Baniso -3
1--7.242 Å20 Å20 Å2
2--3.213 Å20 Å2
3---4.028 Å2
Refinement stepCycle: LAST / Resolution: 2.1→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2782 545 40 252 3619
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.74
LS refinement shellResolution: 2.1→2.14 Å /
RfactorNum. reflection
Rfree0.432 50
Rwork0.319 -
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 500 Å / σ(F): 0 / Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.7 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.432 / Rfactor Rwork: 0.319

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