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- PDB-4f2s: DNA Polymerase I Large Fragment complex 4 -

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Basic information

Entry
Database: PDB / ID: 4f2s
TitleDNA Polymerase I Large Fragment complex 4
Components
  • DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
  • DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
  • DNA polymerase
KeywordsTransferase/DNA / DNA Polymerase I / protein-DNA complex / closed form / Transferase-DNA complex
Function / homology
Function and homology information


5'-3' exonuclease activity / double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 ...DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / PIN-like domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
sucrose / CYTIDINE-5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.651 Å
AuthorsWang, W. / Beese, L.S.
Citation
Journal: to be published
Title: Structures of a High-fidelity DNA Polymerase
Authors: Wang, W. / Hellinga, H.W. / Beese, L.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.
Authors: Wang, W. / Hellinga, H.W. / Beese, L.S.
History
DepositionMay 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
D: DNA polymerase
B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
C: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
F: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,16712
Polymers148,3656
Non-polymers1,8026
Water23,8341323
1
A: DNA polymerase
B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
C: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0085
Polymers74,1833
Non-polymers8252
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-20 kcal/mol
Surface area26930 Å2
MethodPISA
2
D: DNA polymerase
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
F: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1597
Polymers74,1833
Non-polymers9764
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-35 kcal/mol
Surface area26970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.180, 108.590, 150.990
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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DNA chain , 2 types, 4 molecules BECF

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


Mass: 2635.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA Primer Strand / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')


Mass: 4056.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA Template Strand / Source: (synth.) synthetic construct (others)

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Protein / Sugars , 2 types, 4 molecules AD

#1: Protein DNA polymerase


Mass: 67490.289 Da / Num. of mol.: 2 / Fragment: unp residues 287-878 / Mutation: D598A, F710Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Gene: polA, GK2730 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q5KWC1, DNA-directed DNA polymerase
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1327 molecules

#5: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1323 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLUS SPECIES WHOSE SEQUENCE IS ...AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLUS SPECIES WHOSE SEQUENCE IS NOT AVAILABLE IN THE UNIPROT DATABASE. IT DIFFERS FROM UNP Q5KWC1 BY THIS SINGLE RESIDUE

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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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 47%-49% Saturated Ammonium Sulfate, 2.5% MPD, 10mM MnSO4, 100mM MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 180667 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 29.445 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.65-1.750.5093.7214735426285189.1
1.75-1.870.3156.15170653275611100
1.87-2.020.3299.94300625259451100
2.02-2.210.19914.7283262235691100
2.21-2.480.14418.56267126223161100
2.48-2.860.11521.78224825189081100
2.86-3.50.09625.32188105161671100
3.5-4.940.08429.31144279126691100
4.94-500.07931.96799517247199.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1026refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4F2R

4f2r


Resolution: 1.651→34.19 Å / Occupancy max: 1 / Occupancy min: 0.13 / SU ML: 0.15 / σ(F): 2.35 / Phase error: 19.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 7731 4.4 %Inherited free reflections from 4F2R
Rwork0.174 ---
obs0.1751 175745 95.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.87 Å2 / Biso min: 6.81 Å2
Refinement stepCycle: LAST / Resolution: 1.651→34.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9310 832 110 1323 11575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110594
X-RAY DIFFRACTIONf_angle_d1.40314535
X-RAY DIFFRACTIONf_chiral_restr0.0941644
X-RAY DIFFRACTIONf_plane_restr0.0071723
X-RAY DIFFRACTIONf_dihedral_angle_d15.2934123
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6511-1.66990.29561200.28342414253442
1.6699-1.68950.25882550.23015243549890
1.6895-1.71010.25522600.22085285554592
1.7101-1.73180.23162640.21425348561293
1.7318-1.75460.27542680.21415411567994
1.7546-1.77860.22432680.20375449571794
1.7786-1.8040.22332830.19715493577695
1.804-1.83090.23042830.20425485576895
1.8309-1.85960.23722760.20025566584296
1.8596-1.890.22972850.18935543582896
1.89-1.92260.23372910.18355592588397
1.9226-1.95760.21562890.18185668595798
1.9576-1.99520.19021990.17575759595898
1.9952-2.0360.21732070.17355790599799
2.036-2.08020.18522100.17185776598699
2.0802-2.12860.20932340.16865818605299
2.1286-2.18180.19452230.16445812603599
2.1818-2.24080.19472730.16585771604499
2.2408-2.30670.20182130.158958826095100
2.3067-2.38120.19122290.15945821605099
2.3812-2.46620.19712450.163558506095100
2.4662-2.5650.18462320.166258776109100
2.565-2.68170.19452520.174358356087100
2.6817-2.8230.22242580.181258716129100
2.823-2.99970.22552870.186158776164100
2.9997-3.23120.19612940.182658556149100
3.2312-3.55610.18983060.166258666172100
3.5561-4.06990.16832990.154159336232100
4.0699-5.12490.16853120.146459526264100
5.1249-34.19720.20183160.191861726488100
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)
10.923-0.09880.13741.85131.21351.739-0.07430.156-0.12840.47530.03180.28340.52550.09680.02980.4150.05460.09910.1820.05940.2046117.2252-51.88628.8288
20.7669-0.5423-0.09633.5320.51610.7311-0.0768-0.1038-0.0157-0.0004-0.16420.9840.2112-0.15470.24650.3672-0.00930.07640.2321-0.06160.4361104.0421-23.654449.323
30.8166-0.0497-0.59532.2160.70962.7065-0.0396-0.22180.16050.26020.1875-0.2101-0.05560.6121-0.12060.19570.0104-0.01110.3622-0.0110.172129.6024-26.414437.8222
41.9305-0.12550.59831.65680.48561.45870.11550.128-0.3595-0.03830.0337-0.12030.21570.1579-0.11030.10680.031-0.02780.1004-0.03130.1594137.0489-47.7367-9.2613
50.71790.4045-0.35971.271-0.26760.7667-0.04640.33370.151-0.3960.15620.1081-0.0918-0.2068-0.09820.21350.0267-0.00130.2290.04640.144121.8924-20.1848-31.0593
60.9038-0.02790.07360.96860.40120.96020.02920.10610.1924-0.0707-0.05440.0734-0.1358-0.07480.01990.07770.01070.00990.10880.0150.1203117.4713-17.6778-8.6237
74.4323-0.53680.17181.3815-0.36692.3683-0.4213-0.01810.23-0.14340.07240.4967-0.0587-0.18630.3590.2938-0.01650.00280.1708-0.04360.3727107.9798-27.827840.4473
83.14230.1608-1.1281.23910.31261.99780.0407-0.12540.3618-0.0176-0.17650.6521-0.0257-0.03410.1280.2165-0.00690.04590.1929-0.00690.3368109.2267-27.81338.2225
94.64831.0723-2.521.462-0.07514.4762-0.18480.37770.035-0.01350.2188-0.34090.108-0.1449-0.05230.17970.03950.03490.12330.02540.1927129.0332-18.4917-27.3393
101.1246-0.8094-0.60860.8294-0.2022.09040.14580.21670.2873-0.36130.0709-0.4661-0.43250.0341-0.22050.2083-0.02020.08680.17360.02630.2074130.5671-17.3855-24.2779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 299:522)A299 - 522
2X-RAY DIFFRACTION2chain 'A' and (resseq 523:604)A523 - 604
3X-RAY DIFFRACTION3chain 'A' and (resseq 605:876)A605 - 876
4X-RAY DIFFRACTION4chain 'D' and (resseq 294:467)D294 - 467
5X-RAY DIFFRACTION5chain 'D' and (resseq 468:604)D468 - 604
6X-RAY DIFFRACTION6chain 'D' and (resseq 605:876)D605 - 876
7X-RAY DIFFRACTION7chain 'B' and (resseq 21:29)B21 - 101
8X-RAY DIFFRACTION8chain 'C' and (resseq 2:12)C2 - 12
9X-RAY DIFFRACTION9chain 'E' and (resseq 21:29)E21 - 101
10X-RAY DIFFRACTION10chain 'F' and (resseq 1:12)F1 - 12

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