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Basic information

Entry
Database: PDB / ID: 2imw
TitleMechanism of Template-Independent Nucleotide Incorporation Catalyzed by a Template-Dependent DNA Polymerase
Components
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'
  • 5'-D(*TP*AP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
  • DNA polymerase IV
KeywordsTransferase/DNA / blunt end DNA Y-family polymerase DNA replication / 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, 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
2',3'-dideoxyadenosine triphosphate / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLing, H. / Yang, W.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Mechanism of Template-independent Nucleotide Incorporation Catalyzed by a Template-dependent DNA Polymerase.
Authors: Fiala, K.A. / Brown, J.A. / Ling, H. / Kshetry, A.K. / Zhang, J. / Taylor, J.S. / Yang, W. / Suo, Z.
History
DepositionOct 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Aug 30, 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_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_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
S: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'
T: 5'-D(*TP*AP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
P: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,23712
Polymers48,3093
Non-polymers9289
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.057, 101.857, 52.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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DNA chain , 2 types, 2 molecules ST

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


Mass: 4096.670 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*AP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'


Mass: 4464.912 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules P

#3: Protein DNA polymerase IV / / Pol IV


Mass: 39747.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: dbin / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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Non-polymers , 4 types, 249 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DDS / 2',3'-dideoxyadenosine triphosphate


Mass: 475.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O11P3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG3350, 0.1 M Calcium acetate, 0.1 M hepes pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG335011
2Calcium acetate11
3hepes11
4H2O11
5PEG335012
6Calcium acetate12
7hepes12

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 31, 2002 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 32881 / % possible obs: 97.5 % / Rmerge(I) obs: 0.063 / Χ2: 1.098 / Net I/σ(I): 16.7
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.090.3415700.7193.7
2.09-2.120.28316190.747199
2.12-2.160.25216410.78199.6
2.16-2.210.22616600.819199.9
2.21-2.260.19316630.8791100
2.26-2.310.16316571.012199.9
2.31-2.370.13816691.057199.9
2.37-2.430.12416701.0551100
2.43-2.50.10916671.117199.9
2.5-2.580.10316481.265199.9
2.58-2.670.09716801.112199.8
2.67-2.780.08916741.174199.8
2.78-2.910.08216831.246199.5
2.91-3.060.07716721.326199.5
3.06-3.250.07316741.352199.2
3.25-3.50.06616751.36198.1
3.5-3.860.0616501.327198
3.86-4.410.05916351.262194.3
4.41-5.550.05316061.207192.5
5.55-300.04414680.954179.2

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Phasing

Phasing MRMethod translation: &STRIP%trans_method

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT2data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1JX4

1jx4


Resolution: 2.05→26.73 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.169 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 954 2.9 %RANDOM
Rwork0.23 ---
obs0.232 32833 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.315 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å20 Å20 Å2
2---1.89 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.05→26.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 568 55 240 3651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223556
X-RAY DIFFRACTIONr_angle_refined_deg1.3032.2064904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6185357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8823.689122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59215579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4571524
X-RAY DIFFRACTIONr_chiral_restr0.0760.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022387
X-RAY DIFFRACTIONr_nbd_refined0.2230.21571
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22400
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2274
X-RAY DIFFRACTIONr_metal_ion_refined0.1480.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.218
X-RAY DIFFRACTIONr_mcbond_it1.2311.51837
X-RAY DIFFRACTIONr_mcangle_it1.37222872
X-RAY DIFFRACTIONr_scbond_it2.532138
X-RAY DIFFRACTIONr_scangle_it3.1144.52032
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 58 -
Rwork0.335 2246 -
obs-2304 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)
10.52510.37430.80320.31650.43151.62910.01150.12260.01810.06290.012-0.02460.0722-0.1446-0.0234-0.02410.0086-0.00070.0269-0.0273-0.049613.78246.955831.1285
22.120.9309-0.64971.2882-0.27110.9678-0.22420.37910.3208-0.14060.1456-0.0744-0.1063-0.03880.0787-0.0557-0.0603-0.07080.00810.1249-0.020331.997630.536136.513
30.81820.79650.69521.68690.50210.89810.04150.3062-0.28570.0220.0814-0.44850.10310.2188-0.1228-0.08230.02440.0082-0.0027-0.03830.048934.82939.288637.279
42.99840.5441.18492.4153-1.0383.1295-0.0754-0.0070.1917-0.1755-0.03140.10860.2352-0.26110.1068-0.0767-0.03240.0239-0.0205-0.0203-0.04747.391516.880355.5273
50.73190.2012-0.6021.38560.64330.9870.01810.03930.1101-0.0066-0.1485-0.20930.0784-0.20970.13030.0898-0.0242-0.075-0.0976-0.0197-0.01420.619730.128852.8737
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PC11 - 7711 - 77
22PC167 - 240167 - 240
33PC1 - 101 - 10
43PC78 - 16678 - 166
54PC241 - 341241 - 341
65SA1801 - 18131 - 13
75TB1906 - 19183 - 15

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