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- PDB-4qwd: TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM... -

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Basic information

Entry
Database: PDB / ID: 4qwd
TitleTERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND (-)3TC-PPNP
Components
  • DNA (5'-D(P*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3')
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / Y-FAMILY DNA POLYMERASE / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


error-prone translesion synthesis / DNA-templated DNA replication / DNA-directed DNA polymerase / damaged DNA binding / 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
Chem-3TT / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGaur, V. / 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_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_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_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
C: DNA (5'-D(P*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3')
D: DNA (5'-D(P*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)49,5958
Polymers48,9663
Non-polymers6295
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-57 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.544, 102.483, 52.375
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-705-

CA

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase IV / Pol IV


Mass: 40090.664 Da / Num. of mol.: 1 / Fragment: Dpo4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (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, 2 molecules CD

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


Mass: 3976.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RANDOM SEQUENCE, CHEMICALLY SYNTHESIZED
#3: DNA chain DNA (5'-D(P*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3')


Mass: 4899.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RANDOM SEQUENCE, CHEMICALLY SYNTHESIZED

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Non-polymers , 3 types, 276 molecules

#4: Chemical ChemComp-3TT / [[[[(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid


Mass: 468.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15N4O11P3S
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% PEG 3350 100MM CALCIUM ACETATE 2.5% GLYCEROL 0.1M MES, PH 7.0, 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
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 25, 2011
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.05→19.92 Å / Num. obs: 32480 / % possible obs: 97.3 % / Observed criterion σ(I): 3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.9
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 2.5 / % possible all: 94

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→19.71 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 14.412 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2985 10 %RANDOM
Rwork0.225 ---
obs0.229 26998 89.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20 Å2
2---0.71 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 593 31 271 3638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223474
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5932.2174801
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.485340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46923.636121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79615563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3281524
X-RAY DIFFRACTIONr_chiral_restr0.1050.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212326
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.5281.51698
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.73522760
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17131776
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.644.52041
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.24433479
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 154 -
Rwork0.379 1523 -
obs--68.9 %
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)
10.50320.2120.24390.16140.15090.1519-0.01380.11560.01660.02540.01270.00430.0150.02810.00110.0178-0.018-0.00430.0580.01740.0131-25.740215.4546-11.3848
21.68667.3676.182332.191527.020222.6819-0.0889-0.0003-0.039-0.58290.0907-0.0978-0.47970.052-0.00180.05920.05840.13060.15310.23190.4112-26.427611.3018-17.5741
30.1281-0.1693-0.11680.63080.33120.19890.05770.0430.02990.0337-0.0682-0.050.0042-0.06380.01060.0769-0.0010.00740.0335-0.0220.0914-30.340828.4463-1.0506
40.24270.11140.14510.11020.11020.1205-0.02430.07170.01110.02290.01110.02090.0080.02050.01320.0452-0.01440.00980.05840.01890.0208-26.382618.016-8.7568
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 341
2X-RAY DIFFRACTION1A702 - 705
3X-RAY DIFFRACTION2A701
4X-RAY DIFFRACTION3D3 - 18
5X-RAY DIFFRACTION3C1 - 13
6X-RAY DIFFRACTION4A801 - 1003
7X-RAY DIFFRACTION4C101 - 129
8X-RAY DIFFRACTION4D101 - 138

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