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- PDB-1s9f: DPO with AT matched -

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Basic information

Entry
Database: PDB / ID: 1s9f
TitleDPO with AT matched
Components
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-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 / 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'-DIDEOXYCYTOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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_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_asym_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_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*A)-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*A)-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*A)-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*A)-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)200,71024
Polymers198,96812
Non-polymers1,74212
Water20,3391129
1
E: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-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)50,1786
Polymers49,7423
Non-polymers4363
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-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)50,1786
Polymers49,7423
Non-polymers4363
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-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)50,1786
Polymers49,7423
Non-polymers4363
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-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)50,1786
Polymers49,7423
Non-polymers4363
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.800, 100.300, 110.800
Angle α, β, γ (deg.)90.00, 95.20, 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*A)-3'


Mass: 4105.685 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 / 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 , 4 types, 1141 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-DDY / 2',3'-DIDEOXYCYTOSINE-5'-DIPHOSPHATE / DDCDP


Mass: 371.178 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15N3O9P2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1129 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
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
1ammonium acetate11
2calcium acetate11
3glycerol11
4PEG 335011
5ADA11
6PEG 335012
7ADA12
8calcium acetate12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 22, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. all: 155631 / Num. obs: 148618 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.205 / Net I/σ(I): 20.2
Reflection shellResolution: 1.99→2.06 Å / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.2 / % possible all: 68.6

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Processing

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

1jx4


Resolution: 2→30 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3529 2.6 %RANDOM
Rwork0.205 ---
all0.212 303646 --
obs0.213 135485 44.6 %-
Solvent computationSolvent model: bulk solvent / Bsol: 50.5232 Å2 / ksol: 0.373044 e/Å3
Displacement parametersBiso mean: 33.89 Å2
Baniso -1Baniso -2Baniso -3
1--4.44 Å20 Å2-1.04 Å2
2--2.94 Å20 Å2
3---1.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10934 2436 100 1129 14599
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_torsion_deg20.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.97
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 (%)
2-2.090.2732792.50.232106860.01628.8
2.09-2.20.2583942.60.216146720.01339.7
2.2-2.340.2654342.60.217161170.01343.5
2.34-2.520.2744472.60.219170560.01346.1
2.52-2.770.2674672.60.222177000.01247.8
2.77-3.170.2554852.60.219182990.01249.4
3.17-40.2415102.70.198186400.01150.5
4-300.25132.70.186187860.00950.8
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 DIFFRACTION5cdi.parcdi.top

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