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- PDB-4qwc: Ternary Crystal Structures of a Y-family DNA polymerase DPO4 from... -

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Entry
Database: PDB / ID: 4qwc
TitleTernary Crystal Structures of a Y-family DNA polymerase DPO4 from Sulfobus Solfataricus in Comples with DNA and L-DCDP
Components
  • DNA (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3')
  • DNA (5'-D(*TP*TP*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3')
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / Y-FAMILY DNA POLYMERASE / TRANSFERASE-DNA COMPLEX / polymerase
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
ACETATE ION / Chem-LTP / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSaccharolobus solfataricus P2 (archaea)
Synthetic DNA (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVyas, R. / Suo, Z.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase.
Authors: Gaur, V. / Vyas, R. / Fowler, J.D. / Efthimiopoulos, G. / Feng, J.Y. / Suo, Z.
History
DepositionJul 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 2.0Apr 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_src_gen / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _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.title / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 2.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3')
C: DNA (5'-D(*TP*TP*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3')
D: DNA polymerase IV
E: DNA (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3')
F: DNA (5'-D(*TP*TP*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,52816
Polymers97,3766
Non-polymers1,15210
Water3,153175
1
A: DNA polymerase IV
B: DNA (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3')
C: DNA (5'-D(*TP*TP*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2738
Polymers48,6883
Non-polymers5855
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-54 kcal/mol
Surface area20240 Å2
MethodPISA
2
D: DNA polymerase IV
E: DNA (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3')
F: DNA (5'-D(*TP*TP*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2548
Polymers48,6883
Non-polymers5665
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-57 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.440, 101.930, 105.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein DNA polymerase IV / / Pol IV


Mass: 39219.715 Da / Num. of mol.: 2 / Fragment: Dpo4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus P2 (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: dbh, dpo4, SSO2448 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules BECF

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


Mass: 3960.600 Da / Num. of mol.: 2 / Fragment: DNA / Source method: obtained synthetically / Source: (synth.) Synthetic DNA (others)
#3: DNA chain DNA (5'-D(*TP*TP*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3')


Mass: 5507.565 Da / Num. of mol.: 2 / Fragment: DNA / Source method: obtained synthetically / Source: (synth.) Synthetic DNA (others)

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Non-polymers , 4 types, 185 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-LTP / 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one


Type: DNA linking / Mass: 387.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N3O10P2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16% PEG 3350, 0.1 M HEPES (PH 7.0), 100MM CALCIUM ACETATE, 2.5% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 18, 2012
RadiationMonochromator: KOHZU HLD-4 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.4→49.22 Å / Num. obs: 41845 / % possible obs: 99.3 %
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10 % / Rmerge(I) obs: 0.892 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FO3

4fo3
PDB Unreleased entry


Resolution: 2.4→46.46 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 23.362 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.42 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27705 2110 5.1 %RANDOM
Rwork0.22728 ---
obs0.22983 39665 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.557 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0 Å2-0 Å2
2--0.3 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5504 1108 101 175 6888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0186923
X-RAY DIFFRACTIONr_bond_other_d0.0060.026371
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.8419543
X-RAY DIFFRACTIONr_angle_other_deg1.239314720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8355682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81623.689244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.791151130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.171548
X-RAY DIFFRACTIONr_chiral_restr0.0740.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021480
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1094.4532737
X-RAY DIFFRACTIONr_mcbond_other2.1094.4522735
X-RAY DIFFRACTIONr_mcangle_it3.5876.6713414
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1735.1894186
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 133 -
Rwork0.327 2906 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7577-0.7932-0.13040.9223-0.45881.31740.0408-0.36410.1075-0.1127-0.018-0.10820.04520.0142-0.02290.02910.00670.00960.220.02480.0344-1.8269-15.821511.9047
21.299-1.2165-0.45341.636-0.07461.67260.127-0.29890.0148-0.19550.0542-0.098-0.09560.0044-0.18120.040.02930.03990.26240.11140.0761-2.385-15.531-40.9103
31.1158-1.11380.05924.35113.47444.06260.2676-0.3293-0.1975-0.72140.1932-0.3633-0.4484-0.1191-0.46080.2726-0.05750.05280.14720.12170.2571-3.0463-30.61620.0622
43.1266-2.7443-3.46992.70813.52474.87580.4826-0.1442-0.0936-0.3991-0.0278-0.2921-0.3688-0.2378-0.45480.1911-0.0661-0.04770.21090.15460.4868-3.8771-31.1524-53.8453
51.14780.05410.35093.21970.82710.50720.1101-0.15280.00390.05-0.2421-0.34350.0978-0.17990.1320.23860.04620.08050.1175-0.03810.2607-6.1424-27.96320.8914
64.1892-3.4122-2.89236.09984.95694.1173-0.2677-0.6646-0.73130.197-0.12610.38360.0955-0.02470.39380.20450.06220.00580.27940.18710.1772-6.6616-27.9874-52.1415
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 342
2X-RAY DIFFRACTION1A401 - 405
3X-RAY DIFFRACTION1A501 - 579
4X-RAY DIFFRACTION2D1 - 342
5X-RAY DIFFRACTION2D401 - 405
6X-RAY DIFFRACTION2D501 - 557
7X-RAY DIFFRACTION3B1 - 13
8X-RAY DIFFRACTION3B201 - 209
9X-RAY DIFFRACTION4E1 - 13
10X-RAY DIFFRACTION4E201 - 205
11X-RAY DIFFRACTION5C4 - 18
12X-RAY DIFFRACTION5A580
13X-RAY DIFFRACTION5C101 - 114
14X-RAY DIFFRACTION6F4 - 18
15X-RAY DIFFRACTION6F101 - 110

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