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- PDB-4gc7: Crystal structure of Dpo4 in complex with S-MC-dADP opposite dT -

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Basic information

Entry
Database: PDB / ID: 4gc7
TitleCrystal structure of Dpo4 in complex with S-MC-dADP opposite dT
Components
  • DNA (5'-D(*G*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3')
  • DNA (5'-D(*TP*CP*AP*TP*GP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
  • DNA polymerase IV
KeywordsTRANSFERASE/RNA / DNA polymerase / TRANSFERASE-RNA complex
Function / homology
Function and homology information


SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol
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
South-methanocarba-2'-deoxyadenosine triphosphate / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsEoff, R.L. / Ketkar, A. / Banerjee, S. / Zafar, M.K.
CitationJournal: Biochemistry / Year: 2012
Title: Differential furanose selection in the active sites of archaeal DNA polymerases probed by fixed-conformation nucleotide analogues.
Authors: Ketkar, A. / Zafar, M.K. / Banerjee, S. / Marquez, V.E. / Egli, M. / Eoff, R.L.
History
DepositionJul 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _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
A: DNA polymerase IV
B: DNA polymerase IV
C: DNA (5'-D(*G*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3')
D: DNA (5'-D(*TP*CP*AP*TP*GP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
E: DNA (5'-D(*G*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3')
F: DNA (5'-D(*TP*CP*AP*TP*GP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,36017
Polymers101,9966
Non-polymers1,36311
Water1,17165
1
A: DNA polymerase IV
C: DNA (5'-D(*G*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3')
D: DNA (5'-D(*TP*CP*AP*TP*GP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7009
Polymers50,9983
Non-polymers7026
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-33 kcal/mol
Surface area20570 Å2
MethodPISA
2
B: DNA polymerase IV
E: DNA (5'-D(*G*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3')
F: DNA (5'-D(*TP*CP*AP*TP*GP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6608
Polymers50,9983
Non-polymers6625
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-40 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.717, 101.085, 99.986
Angle α, β, γ (deg.)90.00, 92.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase IV / Pol IV


Mass: 41224.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: P2 / Gene: dbh, dpo4, SSO2448 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules CEDF

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


Mass: 4385.852 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized oligonucleotide
#3: DNA chain DNA (5'-D(*TP*CP*AP*TP*GP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')


Mass: 5387.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized oligonucleotide

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Non-polymers , 3 types, 76 molecules

#4: Chemical ChemComp-0OJ / South-methanocarba-2'-deoxyadenosine triphosphate


Mass: 501.220 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N5O11P3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20 mM Tris HCl (pH 8.0), 15% PEG3350, 60 mM NaCl, 5 mM magnesium chloride, 4% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2011
RadiationMonochromator: Si(220) Side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. all: 22641 / Num. obs: 21258 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 60.9 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1829 / % possible all: 63

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T5J

3t5j


Resolution: 2.89→47.478 Å / SU ML: 0.42 / σ(F): 0 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 1860 8.75 %RANDOM
Rwork0.2062 ---
all0.2114 21258 --
obs0.2114 21258 90.12 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.121 Å2 / ksol: 0.303 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.6596 Å20 Å2-4.7595 Å2
2--1.8084 Å2-0 Å2
3---7.7929 Å2
Refinement stepCycle: LAST / Resolution: 2.89→47.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5486 1161 63 65 6775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016924
X-RAY DIFFRACTIONf_angle_d1.3839568
X-RAY DIFFRACTIONf_dihedral_angle_d20.8222791
X-RAY DIFFRACTIONf_chiral_restr0.0761088
X-RAY DIFFRACTIONf_plane_restr0.0051004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.96780.3652990.33271036X-RAY DIFFRACTION63
2.9678-3.05510.39471250.29851365X-RAY DIFFRACTION83
3.0551-3.15370.33221430.27331384X-RAY DIFFRACTION85
3.1537-3.26630.28881400.24721496X-RAY DIFFRACTION90
3.2663-3.39710.32141560.23741485X-RAY DIFFRACTION91
3.3971-3.55170.31541320.22681558X-RAY DIFFRACTION93
3.5517-3.73880.27271690.20371545X-RAY DIFFRACTION94
3.7388-3.9730.27871410.19911557X-RAY DIFFRACTION95
3.973-4.27950.26861530.17841584X-RAY DIFFRACTION96
4.2795-4.70990.21471480.15571600X-RAY DIFFRACTION96
4.7099-5.39060.23631430.18161597X-RAY DIFFRACTION96
5.3906-6.78840.29851550.2221599X-RAY DIFFRACTION95
6.7884-47.48470.20281560.19531592X-RAY DIFFRACTION94

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