[English] 日本語
Yorodumi
- PDB-4b9l: Structure of the high fidelity DNA polymerase I with the oxidativ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b9l
TitleStructure of the high fidelity DNA polymerase I with the oxidative formamidopyrimidine-dA DNA lesion in the pre-insertion site.
Components
  • 5'-D(*CP*AP*GP*FAX*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'
  • 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*TP)-3'
  • DNA POLYMERASE I
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / OXIDATIVE DNA LESION / DNA DAMAGE / TRANS LESION SYNTHESIS / REPLICATION
Function / homology
Function and homology information


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
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 / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. ...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 / 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 / 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 / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGehrke, T.H. / Lischke, U. / Arnold, S. / Schneider, S. / Carell, T.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions.
Authors: Gehrke, T.H. / Lischke, U. / Gasteiger, K.L. / Schneider, S. / Arnold, S. / Muller, H.C. / Stephenson, D.S. / Zipse, H. / Carell, T.
History
DepositionSep 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references / Structure summary
Revision 1.2May 29, 2013Group: Database references
Revision 1.3Jul 3, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA POLYMERASE I
B: 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*TP)-3'
C: 5'-D(*CP*AP*GP*FAX*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8529
Polymers78,1023
Non-polymers7516
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-70.4 kcal/mol
Surface area27400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.528, 93.265, 106.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
DNA chain , 2 types, 2 molecules BC

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


Mass: 2995.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
#3: DNA chain 5'-D(*CP*AP*GP*FAX*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'


Mass: 4659.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein DNA POLYMERASE I


Mass: 70446.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Description: GERMAN COLLECTION OF MICROORGANISMS DSM NO. 22 / Plasmid: PDEST007 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: E1C9K5, 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.: 1
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

-
Non-polymers , 3 types, 232 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsCHAIN C RESIDUES 1-3 AND 15 DISORDERED

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 56.84 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→45.37 Å / Num. obs: 55071 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 4.2 % / Biso Wilson estimate: 25.35 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.6
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U45

1u45


Resolution: 2.05→41.156 Å / SU ML: 0.5 / σ(F): 0 / Phase error: 22.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 2758 5 %
Rwork0.1886 --
obs0.1905 54997 99.74 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.224 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.9087 Å20 Å20 Å2
2---3.1645 Å20 Å2
3----7.7442 Å2
Refinement stepCycle: LAST / Resolution: 2.05→41.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4653 432 44 227 5356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095293
X-RAY DIFFRACTIONf_angle_d1.2127257
X-RAY DIFFRACTIONf_dihedral_angle_d17.612057
X-RAY DIFFRACTIONf_chiral_restr0.078821
X-RAY DIFFRACTIONf_plane_restr0.005863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.08540.28491400.26072585X-RAY DIFFRACTION100
2.0854-2.12330.34521370.23942555X-RAY DIFFRACTION100
2.1233-2.16410.25861410.23072591X-RAY DIFFRACTION100
2.1641-2.20830.24311310.21472591X-RAY DIFFRACTION100
2.2083-2.25630.28271460.20592572X-RAY DIFFRACTION100
2.2563-2.30880.23591300.19542588X-RAY DIFFRACTION100
2.3088-2.36650.28191310.19942605X-RAY DIFFRACTION100
2.3665-2.43050.25081440.20572550X-RAY DIFFRACTION100
2.4305-2.5020.24861270.19832627X-RAY DIFFRACTION100
2.502-2.58270.24641420.2032583X-RAY DIFFRACTION100
2.5827-2.6750.251390.19572596X-RAY DIFFRACTION100
2.675-2.78210.23911340.20452605X-RAY DIFFRACTION100
2.7821-2.90870.25571370.20022615X-RAY DIFFRACTION100
2.9087-3.0620.24061360.21522614X-RAY DIFFRACTION100
3.062-3.25380.23361360.20092617X-RAY DIFFRACTION100
3.2538-3.50490.20731400.18182624X-RAY DIFFRACTION100
3.5049-3.85740.2051370.16592632X-RAY DIFFRACTION100
3.8574-4.4150.17131400.1492662X-RAY DIFFRACTION100
4.415-5.56020.18381410.15352672X-RAY DIFFRACTION100
5.5602-41.16420.20771490.18552755X-RAY DIFFRACTION98
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)
10.1580.01340.10280.30680.09410.2218-0.05740.2330.0191-0.22940.0930.0254-0.0253-0.09740.00020.2066-0.0393-0.00540.1772-0.00680.131-10.415718.4544-54.8968
20.3520.0914-0.00610.2383-0.23830.3329-0.0085-0.00120.0235-0.01390.0092-0.0114-0.03740.012-0.00010.1128-0.0122-0.00630.1212-0.00460.1152-8.763719.2957-40.4096
30.12510.0739-0.19380.2143-0.04280.2696-0.13870.0576-0.06240.34010.08830.12710.0926-0.2469-0.00050.34540.04870.03220.3073-0.02760.2031-38.89957.63-10.3903
40.1965-0.03350.00340.0834-0.02670.05750.04-0.0291-0.00340.0706-0.030.10230.05140.013-00.1277-0.0245-0.01690.1353-0.02150.1676-22.5070.4611-29.0924
50.28410.2236-0.08530.15480.00550.21550.04630.00660.14810.1610.09340.1338-0.1419-0.0330.00840.15510.02530.05640.10860.02880.1418-6.17531.063-3.2869
60.43630.2084-0.00680.4489-0.17990.14720.0624-0.0150.00970.1259-0.03180.0252-0.02390.0362-0.00010.1482-0.0097-0.00130.126-0.00890.1235-3.60074.396-20.249
70.0042-0.0027-0.00970.00330.00750.01720.0455-0.235-0.08520.13370.21920.0486-0.0167-0.0519-0.00010.2388-0.04920.03250.1756-0.00960.2038-22.1996-11.127-25.4083
80.0106-0.01350.01780.0679-0.06280.06020.02130.06670.0394-0.0386-0.00120.0824-0.07490.11790.07240.84940.23410.15860.60750.31590.5611-30.822625.4285-23.4434
90.0241-0.0209-0.00830.01810.00160.01480.00490.0591-0.1810.3449-0.02720.0862-0.22260.07680.00030.3702-0.0030.1030.19240.00640.2841-25.37259.5455-15.7761
100.043-0.0009-0.05040.0414-0.00830.05220.0460.00680.10820.2681-0.0131-0.0008-0.3136-0.1038-0.00010.30720.0277-0.02990.277-0.02960.2359-20.365312.7971-20.6937
110.093-0.0298-0.02650.01890.03620.0881-0.00890.03470.15920.09640.01220.047-0.1435-0.0833-0.00090.61310.55730.02280.31280.16150.4153-37.976420.7732-19.9443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 297:368)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 369:494)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 495:585)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 586:654)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 655:732)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 733:868)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 869:876)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 1:4)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 5:10)
10X-RAY DIFFRACTION10(CHAIN C AND RESID 5:10)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 11:14)

+
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