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- PDB-4g3i: Crystal structure of Dpo4 in complex with DNA duplex -

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Basic information

Entry
Database: PDB / ID: 4g3i
TitleCrystal structure of Dpo4 in complex with DNA duplex
Components
  • (DNA) x 2
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / DNA synthesis / 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
DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYan, Y.Y. / Gan, J.H. / Huang, Z.
CitationJournal: To be Published
Title: Crystal structure of Dpo4 in complex with DNA duplex
Authors: Yan, Y.Y. / Gan, J.H. / Huang, Z.
History
DepositionJul 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_ncs_dom_lim / 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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
C: DNA
D: DNA
E: DNA
F: DNA
A: DNA polymerase IV
B: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9158
Polymers95,8356
Non-polymers802
Water36020
1
C: DNA
D: DNA
A: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9574
Polymers47,9173
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-41 kcal/mol
Surface area19010 Å2
MethodPISA
2
E: DNA
F: DNA
B: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9574
Polymers47,9173
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-41 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.472, 52.634, 99.445
Angle α, β, γ (deg.)75.40, 80.35, 70.97
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22E
13D
23F

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILEAE1 - 3412 - 342
21METMETILEILEBF1 - 3412 - 342
12DGDGDCDCCA4 - 137 - 16
22DGDGDCDCEC4 - 137 - 16
13DGDGDGDGDB5 - 121 - 8
23DGDGDGDGFD5 - 121 - 8

NCS ensembles :
ID
1
2
3

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Components

#1: DNA chain DNA


Mass: 4834.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA


Mass: 3976.599 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein DNA polymerase IV / Pol IV


Mass: 39106.598 Da / Num. of mol.: 2
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: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97W02, DNA-directed DNA polymerase
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 52.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M CaCl2, 0.1 M Na Cacodylate pH 6.5, 19 % PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2010
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→95.813 Å / Num. all: 34376 / Num. obs: 33414 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.083 / Net I/σ(I): 12.4
Reflection shellResolution: 2.48→2.61 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 4951 / Rsym value: 0.297 / % possible all: 96.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AGQ

2agq


Resolution: 2.5→95.81 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.882 / SU B: 25.325 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29363 1650 5.1 %RANDOM
Rwork0.24067 ---
all0.24337 34376 --
obs0.24337 30884 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.155 Å2
Baniso -1Baniso -2Baniso -3
1--2.09 Å22.12 Å20.02 Å2
2--0 Å2-1.51 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.5→95.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5494 722 2 20 6238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226378
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9232.1358720
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7535681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42423.636242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.407151127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3411548
X-RAY DIFFRACTIONr_chiral_restr0.1180.2997
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214410
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_it1.1511.53403
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.02625532
X-RAY DIFFRACTIONr_scbond_it2.68932975
X-RAY DIFFRACTIONr_scangle_it4.1164.53188
X-RAY DIFFRACTIONr_rigid_bond_restr1.55636378
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2744MEDIUM POSITIONAL0.510.5
1A2744MEDIUM THERMAL0.92
2C198MEDIUM POSITIONAL0.50.5
2C198MEDIUM THERMAL0.622
3D163MEDIUM POSITIONAL0.440.5
3D163MEDIUM THERMAL0.752
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 117 -
Rwork0.261 2231 -
obs--96.07 %
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)
10.911-0.4644-0.19711.6181-0.63150.97390.06650.11390.0151-0.25840.0130.16740.1883-0.0096-0.07950.3183-0.0622-0.00220.17680.00490.187519.11999.5501-22.911
21.5128-0.24390.29220.58810.0780.07810.0264-0.0097-0.0056-0.00310.0104-0.0629-0.0471-0.0035-0.03680.1596-0.03060.00140.2611-0.01540.1449-5.427812.260815.4297
33.7112-3.94171.71176.89510.17130.14550.65360.2319-0.0909-1.1353-0.482-0.39110.16810.2568-0.17170.56620.00990.1740.52560.12940.229413.181819.821-29.9825
42.0005-6.96683.281814.9457-1.59563.12030.53250.0296-0.2906-2.2116-0.8018-0.3065-0.1384-0.09380.26930.85660.16060.28580.26910.1180.401914.53916.8256-26.4996
5-0.4182-0.0494-1.90721.32471.38921.4677-0.2256-0.1836-0.07430.38960.2828-0.35330.24540.3185-0.05730.33660.0491-0.1230.3185-0.00490.30542.23382.797222.8284
69.3977-6.2509-6.21743.87494.73733.0981-0.2863-0.83640.77560.46840.6178-0.13050.33140.2982-0.33150.24910.1379-0.12840.5063-0.18110.3445-0.11294.839819.4446
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 341
2X-RAY DIFFRACTION2B1 - 341
3X-RAY DIFFRACTION3C4 - 13
4X-RAY DIFFRACTION4D5 - 12
5X-RAY DIFFRACTION5E4 - 13
6X-RAY DIFFRACTION6F5 - 12

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