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- PDB-3py8: Crystal structure of a mutant of the large fragment of DNA polyme... -

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Basic information

Entry
Database: PDB / ID: 3py8
TitleCrystal structure of a mutant of the large fragment of DNA polymerase I from thermus aquaticus in a closed ternary complex with DNA and ddCTP
Components
  • DNA (5'-D(*AP*A*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
  • DNA polymerase I
KeywordsTransferase/DNA / Modified Klenow fragment / Transferase / polymerase / nucleoside binding / nucleic acid binding / DNA binding / catalytic activity / DNA-directed DNA polymerase activity / 5'-3' exonuclease activity / nucleotides / modified nucleotide / artificial nucleotide / nucleotide probes / Transferase-DNA complex
Function / homology
Function and homology information


nucleoside binding / hydrolase activity, acting on ester bonds / double-strand break repair via alternative nonhomologous end joining / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Taq polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / 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 ...Taq polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / 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 / 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 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 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
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsSchnur, A. / Marx, A. / Welte, W. / Diederichs, K.
CitationJournal: Chembiochem / Year: 2011
Title: Learning from Directed Evolution: Thermus aquaticus DNA Polymerase Mutants with Translesion Synthesis Activity.
Authors: Obeid, S. / Schnur, A. / Gloeckner, C. / Blatter, N. / Welte, W. / Diederichs, K. / Marx, A.
History
DepositionDec 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_leaving_atom_flag / _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_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 I
B: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
C: DNA (5'-D(*AP*A*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,46712
Polymers69,5333
Non-polymers9349
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-41 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.610, 108.610, 90.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-834-

GOL

21A-868-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase I / Taq polymerase 1


Mass: 60950.973 Da / Num. of mol.: 1 / Fragment: DNA polymerase I large fragment / Mutation: I614K, M747K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: polA, pol1 / Plasmid: pASK-IBA37plus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: P19821, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules BC

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


Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*A*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4964.216 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 5 types, 532 molecules

#4: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.1M Hepes, 20mM MnCl2, 0.1M Na-acetate, 12 % PEG 4000, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1Hepes11
2MnCl211
3Na-acetate11
4PEG 400011
5Hepes12
6MnCl212
7Na-acetate12
8PEG 400012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.74→47 Å / Num. obs: 80053 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Net I/σ(I): 18.7
Reflection shell
Resolution (Å)Mean I/σ(I) obsDiffraction-ID% possible all
1.74-1.791.59199.9
1.79-1.852.351100
1.85-1.923.541100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: dev_572)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→41.738 Å / SU ML: 0.18 / σ(F): 1.99 / Phase error: 19.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1993 3182 5.02 %
Rwork0.1692 --
obs0.1707 63416 99.88 %
all-63432 -
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.311 Å2 / ksol: 0.425 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6339 Å2-0 Å2-0 Å2
2--1.6339 Å2-0 Å2
3----3.2677 Å2
Refinement stepCycle: LAST / Resolution: 1.74→41.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 528 45 523 5380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055008
X-RAY DIFFRACTIONf_angle_d1.0636889
X-RAY DIFFRACTIONf_dihedral_angle_d15.1611942
X-RAY DIFFRACTIONf_chiral_restr0.058754
X-RAY DIFFRACTIONf_plane_restr0.004804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.76610.29851390.27362572X-RAY DIFFRACTION100
1.7661-1.79370.32541180.25742592X-RAY DIFFRACTION99
1.7937-1.82310.28011490.24392565X-RAY DIFFRACTION99
1.8231-1.85450.25471410.23062584X-RAY DIFFRACTION100
1.8545-1.88820.28171440.20212597X-RAY DIFFRACTION100
1.8882-1.92450.24791280.19122576X-RAY DIFFRACTION100
1.9245-1.96380.23821290.18052636X-RAY DIFFRACTION100
1.9638-2.00650.21181260.16932602X-RAY DIFFRACTION100
2.0065-2.05320.23461540.16872585X-RAY DIFFRACTION100
2.0532-2.10450.19561240.16812631X-RAY DIFFRACTION100
2.1045-2.16140.20581460.16092591X-RAY DIFFRACTION100
2.1614-2.2250.21541250.1562603X-RAY DIFFRACTION100
2.225-2.29690.21441230.15642638X-RAY DIFFRACTION100
2.2969-2.37890.20061440.15922597X-RAY DIFFRACTION100
2.3789-2.47420.20931540.16512621X-RAY DIFFRACTION100
2.4742-2.58680.22861330.16372620X-RAY DIFFRACTION100
2.5868-2.72310.19071560.16892608X-RAY DIFFRACTION100
2.7231-2.89370.2311410.17122620X-RAY DIFFRACTION100
2.8937-3.11710.20621530.16662624X-RAY DIFFRACTION100
3.1171-3.43060.1861270.15812649X-RAY DIFFRACTION100
3.4306-3.92670.17841350.14352678X-RAY DIFFRACTION100
3.9267-4.9460.16031590.13982656X-RAY DIFFRACTION100
4.946-41.750.16751340.19732789X-RAY DIFFRACTION100
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)
10.61660.1829-0.10770.3833-0.14220.92280.00130.0455-0.243-0.16130.0164-0.30590.37560.10280.1090.2764-0.04870.06040.1677-0.01790.316842.5567-42.8917-17.5649
20.57370.2551-0.24180.581-0.5090.57740.0444-0.06650.02890.1589-0.05060.0664-0.1492-0.00880.00350.2262-0.06650.03160.1759-0.01190.162433.7199-17.31610.5209
30.2608-0.6048-0.3481.54841.09821.02360.23950.06390.0662-0.002-0.23280.3263-0.3109-0.11770.00930.57630.04160.14380.5166-0.04980.594623.186-3.194413.1723
40.57360.3645-0.33550.7152-0.10521.01410.1124-0.08610.0750.1691-0.0278-0.0739-0.26890.0443-0.07020.2536-0.03170.01460.17990.00520.195738.9061-9.3033-0.5382
50.17590.11780.12960.5077-0.1390.8462-0.07830.07830.0282-0.11620.15830.0291-0.1521-0.3551-0.00310.1382-0.0457-0.00340.2310.01340.135226.99-18.3783-14.3733
60.35490.16420.00880.31470.06530.01670.01960.22560.1116-0.04310.00310.0149-0.03380.0735-0.02720.4380.49540.03340.98780.13850.4773.2494-14.7402-16.5066
71.7076-0.9293-0.34111.0080.27810.75790.00860.04680.0866-0.00430.0466-0.13630.04730.1033-0.03530.59050.1292-0.10790.711-0.06260.63469.2987-7.4242-5.3495
80.1884-0.09630.1630.2905-0.19140.5006-0.00670.0061-0.0081-0.02550.0009-0.01320.0268-0.01570.01451.12990.1356-0.01140.79870.14250.83997.73680.0697-9.3679
90.7083-0.1438-0.13980.03550.0260.02920.07860.0837-0.011-0.0693-0.08490.0269-0.1274-0.2669-0.00920.58520.1781-0.03820.6866-0.00050.430717.1285-5.7601-7.8867
101.89970.0075-0.49942.3538-1.11221.0982-0.1031-0.33990.00870.23090.12950.1118-0.322-0.08-0.03330.55820.1784-0.00920.8093-0.00540.376313.0414-17.54531.5133
110.8964-0.3229-0.60290.50490.50720.828-0.0048-0.2138-0.00080.08990.20710.0306-0.12020.2045-0.18981.06390.3960.31881.1275-0.0910.62339.4847-9.84669.3292
120.22410.0223-0.06720.0857-0.05660.2802-0.0226-0.13880.15430.13280.07040.1662-0.4061-0.5821-0.16160.0863-0.02950.16681.30680.26620.33283.0121-23.2689-1.8384
130.0821-0.0224-0.11760.01420.00970.2329-0.02090.0337-0.056-0.0350.01430.06830.0643-0.1028-0.00550.2175-0.6901-0.03080.52750.31590.46049.2393-42.9079-2.5478
140.5742-0.2490.13950.5750.08460.2654-0.13230.0243-0.0897-0.15230.17960.07670.1064-0.3618-0.21030.1591-0.0963-0.00690.28310.02340.16321.4743-29.0772-12.8715
150.3386-0.2051-0.0120.69610.45180.41640.05430.31980.0758-0.27830.06430.0056-0.2775-0.57420.21230.2541-0.0423-0.03520.39420.0440.153521.5701-15.4753-25.5336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 294:418)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 419:519)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 520:525)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 526:556)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 557:629)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 630:637)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 638:647)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 648:653)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 654:662)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 663:678)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 679:688)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 689:711)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 712:718)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 719:793)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 794:832)

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