[English] 日本語
Yorodumi
- PDB-3po5: Structure of a mutant of the large fragment of DNA polymerase I f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3po5
TitleStructure of a mutant of the large fragment of DNA polymerase I from Thermus Auqaticus in complex with an abasic site and ddATP
Components
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DA))-3')
  • DNA (5'-D(P*(3DR)P*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / DNA polymerase / lesion bypass / apsite / abasic site / 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'-dideoxyadenosine triphosphate / TRIETHYLENE GLYCOL / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsMarx, A. / Diederichs, K. / Obeid, S.
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
DepositionNov 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_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_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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase I
B: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DA))-3')
C: DNA (5'-D(P*(3DR)P*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3358
Polymers68,4433
Non-polymers8925
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-14 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.301, 109.301, 90.318
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-95-

HOH

21A-130-

HOH

31A-131-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase I / Taq polymerase 1


Mass: 60950.973 Da / Num. of mol.: 1 / Fragment: Klenow Fragment / Mutation: I614K, M747K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: pol1, polA, polI / Plasmid: pET21-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P19821, DNA-directed DNA polymerase

-
DNA chain , 2 types, 2 molecules BC

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


Mass: 3641.395 Da / Num. of mol.: 1 / Fragment: DNA primer / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*(3DR)P*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 3850.472 Da / Num. of mol.: 1 / Fragment: DNA template / Source method: obtained synthetically

-
Non-polymers , 5 types, 136 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-DDS / 2',3'-dideoxyadenosine triphosphate


Mass: 475.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O11P3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.05M Tris HCl, 0.2M NH4Cl, 0.01M CaCl2, 28% PEG 4000, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris HCl11
2NH4Cl11
3CaCl211
4PEG 400011
5Tris HCl12
6NH4Cl12
7CaCl212
8PEG 400012

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2010
Details: Dynamically bendable mirror, LN2 cooled fixed-exit, Si(111) monochromator
RadiationMonochromator: LN2 cooled fixed-exit, Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 24927 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.04 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 12.82
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 5.61 % / Mean I/σ(I) obs: 1.24

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_572)model building
PHENIX(phenix.refine: dev_572)refinement
XDSdata reduction
XDSdata scaling
PHENIXdev_572phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LWL

3lwl


Resolution: 2.39→47.33 Å / SU ML: 0.35 / Isotropic thermal model: isotropic and tls / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 1287 5.16 %
Rwork0.21 --
obs0.212 24927 99.7 %
all-24927 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8507 Å20 Å2-0 Å2
2--2.8507 Å2-0 Å2
3----11.6363 Å2
Refinement stepCycle: LAST / Resolution: 2.39→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4197 499 44 131 4871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064886
X-RAY DIFFRACTIONf_angle_d0.9216709
X-RAY DIFFRACTIONf_dihedral_angle_d18.5081914
X-RAY DIFFRACTIONf_chiral_restr0.048735
X-RAY DIFFRACTIONf_plane_restr0.004783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.48780.32841230.28492569X-RAY DIFFRACTION97
2.4878-2.6010.3791470.27962565X-RAY DIFFRACTION100
2.601-2.73810.34621490.27072609X-RAY DIFFRACTION100
2.7381-2.90960.36171370.26752604X-RAY DIFFRACTION100
2.9096-3.13420.33151300.24262617X-RAY DIFFRACTION100
3.1342-3.44960.2391480.2222629X-RAY DIFFRACTION100
3.4496-3.94850.24481560.19262627X-RAY DIFFRACTION100
3.9485-4.97390.21711400.15752658X-RAY DIFFRACTION100
4.9739-47.3380.23061570.1852762X-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)
10.25290.0855-0.11510.0677-0.08280.1349-0.02090.0335-0.2138-0.11270.0451-0.22290.06350.03990.00180.312-0.14260.16230.3133-0.13990.669442.3601-43.1566-17.6372
20.24210-0.20720.4298-0.31210.64460.01920.12850.030.11380.0375-0.0559-0.2991-0.173-0.07170.3675-0.08690.06580.2803-0.01040.249131.1094-16.0637-4.8274
30.8581-0.4455-0.43790.40180.25170.22850.0745-0.0445-0.04670.05130.1143-0.0065-0.20320.0729-0.19010.93350.2848-0.08620.9792-0.08460.5559.1077-13.6834-3.7696
40.850.2492-0.11330.68560.10610.0828-0.00760.1555-0.0685-0.05440.0228-0.02770.3160.1247-0.01621.48440.17770.08591.1945-0.07890.42687.889-12.55087.5615
50.040.03420.00390.08850.03070.0462-0.05340.0117-0.0411-0.10580.06810.0148-0.0632-0.0898-0.04830.0561-0.16690.05750.34350.03070.001918.203-25.7815-14.3715
60.44410.2177-0.16590.5813-0.0730.06560.05010.3718-0.18760.0798-0.1872-0.08940.01210.27490.0860.18380.0689-0.00990.34550.04810.349336.9828-23.15934.1028
70.00240.0118-0.02090.0502-0.10240.3071-0.27580.0143-0.10860.03510.1322-0.15620.04340.02560.13870.20020.0413-0.01540.33650.01490.326837.0625-24.20575.4082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 295:419)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 420:635)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 636:678)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 679:693)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 694:832)
6X-RAY DIFFRACTION6(CHAIN B)
7X-RAY DIFFRACTION7(CHAIN C)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more