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- PDB-1s97: DPO4 with GT mismatch -

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Basic information

Entry
Database: PDB / ID: 1s97
TitleDPO4 with GT mismatch
Components
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*G)-3'
  • 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / PROTEIN-DNA COMPLEX / DNA DUPLEX / G.T MISMATCH / 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, Y-family, little finger domain superfamily ...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'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTrincao, J. / Johnson, R.E. / Wolfle, W.T. / Escalante, C.R. / Prakash, S. / Prakash, L. / Aggarwal, A.K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Dpo4 is hindered in extending a G.T mismatch by a reverse wobble
Authors: Trincao, J. / Johnson, R.E. / Wolfle, W.T. / Escalante, C.R. / Prakash, S. / Prakash, L. / Aggarwal, A.K.
History
DepositionFeb 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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.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_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_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_conn.ptnr2_label_seq_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
E: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*G)-3'
I: 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
F: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*G)-3'
J: 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
G: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*G)-3'
K: 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
H: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*G)-3'
L: 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
A: DNA polymerase IV
B: DNA polymerase IV
C: DNA polymerase IV
D: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,99720
Polymers199,03212
Non-polymers1,9658
Water9,998555
1
E: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*G)-3'
I: 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
A: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2495
Polymers49,7583
Non-polymers4912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*G)-3'
J: 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
B: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2495
Polymers49,7583
Non-polymers4912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*G)-3'
K: 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
C: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2495
Polymers49,7583
Non-polymers4912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*G)-3'
L: 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
D: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2495
Polymers49,7583
Non-polymers4912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.433, 100.644, 110.426
Angle α, β, γ (deg.)90.00, 94.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 8 molecules EFGHIJKL

#1: DNA chain
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*G)-3'


Mass: 4121.684 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: DNA chain
5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'


Mass: 5378.478 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Protein , 1 types, 4 molecules ABCD

#3: Protein
DNA polymerase IV / / 2.7.7.7 / Pol IV


Mass: 40257.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: DBH, DPO4, SSO2448 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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Non-polymers , 3 types, 563 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, ADA, ammonium acetate, calcium acetate, glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1ADA11
2ammonium acetate11
3calcium acetate11
4glycerol11
5H2O11
6ADA12
7glycerol12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.2834 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2834 Å / Relative weight: 1
ReflectionResolution: 2.4→47.01 Å / Num. all: 89233 / Num. obs: 76535 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.2
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JX4:A

1jx4


Resolution: 2.4→29.64 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3866 5.1 %RANDOM
Rwork0.218 ---
all0.236 89095 --
obs0.238 76508 85.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 30.0224 Å2 / ksol: 0.329927 e/Å3
Displacement parametersBiso mean: 32.95 Å2
Baniso -1Baniso -2Baniso -3
1--4.16 Å20 Å2-0.65 Å2
2--2.94 Å20 Å2
3---1.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10898 2436 112 555 14001
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg21
X-RAY DIFFRACTIONx_torsion_impr_deg1.39
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
2.4-2.510.3243945.50.26167790.01664.7
2.51-2.640.3194175.20.25475700.01671.8
2.64-2.810.3194445.10.25183070.01579.1
2.81-3.020.3025065.30.23890690.01386.1
3.02-3.330.2974924.80.23397950.01392.3
3.33-3.810.2635254.90.222102170.01196.5
3.81-4.790.23554450.184104110.0197.9
4.79-29.640.2295444.90.202104940.0197.5
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
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna_repo.top
X-RAY DIFFRACTION5dct.pardct.top

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