[English] 日本語
Yorodumi
- PDB-3l8b: Crystal structure of a replicative DNA polymerase bound to the ox... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3l8b
TitleCrystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin
Components
  • DNA (5'-D(*AP*C*TP*(G35)P*TP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
  • DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*A)-3')
  • DNA polymerase
Keywordstransferase/DNA / DNA polymerase RB69 gp43 / protein-DNA complex / oxidative DNA lesion / guanidinohydantoin / DNA replication / DNA-binding / DNA-directed DNA polymerase / Exonuclease / Hydrolase / Nuclease / Nucleotidyltransferase / Transferase / transferase-DNA complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 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
DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Monooxygenase ...DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Monooxygenase / : / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Helix Hairpins / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsAller, P. / Ye, Y. / Wallace, S.S. / Burrows, C.J. / Doublie, S.
CitationJournal: Biochemistry / Year: 2010
Title: Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin.
Authors: Aller, P. / Ye, Y. / Wallace, S.S. / Burrows, C.J. / Doublie, S.
History
DepositionDec 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase
B: DNA polymerase
C: DNA (5'-D(*AP*C*TP*(G35)P*TP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
D: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*A)-3')
E: DNA (5'-D(*AP*C*TP*(G35)P*TP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
F: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,3608
Polymers229,1686
Non-polymers1922
Water17,979998
1
A: DNA polymerase
C: DNA (5'-D(*AP*C*TP*(G35)P*TP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
D: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)114,5843
Polymers114,5843
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-39 kcal/mol
Surface area43180 Å2
MethodPISA
2
B: DNA polymerase
E: DNA (5'-D(*AP*C*TP*(G35)P*TP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
F: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7765
Polymers114,5843
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-43 kcal/mol
Surface area43000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.276, 120.246, 136.963
Angle α, β, γ (deg.)90.00, 95.96, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein DNA polymerase / Gp43


Mass: 105069.586 Da / Num. of mol.: 2 / Mutation: D222A, D327A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43, gp43 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q38087, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(*AP*C*TP*(G35)P*TP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')


Mass: 5522.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA template
#3: DNA chain DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*A)-3')


Mass: 3991.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA primer
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 998 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Description: The Structure Factor file contains Friedel pairs
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: reservoir: 12% PEG2000MME, 100mM Sodium Acetate, 150mM Magnesium Sulfate, 100mM Hepes pH 7.0, 6% Glycerol and 2mM Beta-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2008
Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.15→48.81 Å / Num. all: 270208 / Num. obs: 239932 / % possible obs: 88.8 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 9.9
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 2 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IG9

1ig9


Resolution: 2.15→48.81 Å / Isotropic thermal model: anisotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 22718 -RANDOM
Rwork0.219 ---
all-270208 --
obs-239932 88.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å24.75 Å2
2---0.54 Å20 Å2
3----0.87 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.15→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14527 1182 10 998 16717
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006266
X-RAY DIFFRACTIONc_angle_deg1.20839

+
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://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