[English] 日本語
Yorodumi
- PDB-2hhw: ddTTP:O6-methyl-guanine pair in the polymerase active site, in th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hhw
TitleddTTP:O6-methyl-guanine pair in the polymerase active site, in the closed conformation
Components
  • 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
  • 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'
  • DNA Polymerase I
KeywordsTransferase/DNA / DNA polymerase I / DNA replication / Klenow fragment / DNA-protein complex / O6-methyl-guanine / Transferase-DNA COMPLEX
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
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 / 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsWarren, J.J. / Forsberg, L.J. / Beese, L.S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: The structural basis for the mutagenicity of O6-methyl-guanine lesions.
Authors: Warren, J.J. / Forsberg, L.J. / Beese, L.S.
History
DepositionJun 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0May 13, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_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_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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.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.type / _pdbx_struct_assembly_gen.asym_id_list / _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_label_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_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Aug 30, 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
Remark 999SEQUENCE THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT UNP SEQUENCE DATABASE AT THE TIME OF ...SEQUENCE THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT UNP SEQUENCE DATABASE AT THE TIME OF PROCESSING. THE SEQUENCE OF THIS PROTEIN IS ANALOGOUS TO GEOBACILLUS KAUSTOPHILUS, UNP ACCESSION, Q5KWC1_GEOKA.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'
F: 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
B: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'
C: 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
A: DNA Polymerase I
D: DNA Polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,71815
Polymers145,7036
Non-polymers2,0159
Water14,304794
1
B: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'
C: 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
A: DNA Polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9078
Polymers72,8513
Non-polymers1,0565
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'
F: 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
D: DNA Polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8117
Polymers72,8513
Non-polymers9594
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.834, 108.897, 150.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains two biological assemblies, each consisting of one protein molecule, two strands of DNA, and an incoming dideoxy thymidine triphosphate. Chains A, B, C, and G constitute one assembly, and chains D, E, F, and G constitute the second.

-
Components

-
DNA chain , 2 types, 4 molecules EBFC

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


Mass: 2675.775 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized
#2: DNA chain 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'


Mass: 4030.650 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized

-
Protein / Sugars , 2 types, 4 molecules AD

#3: Protein DNA Polymerase I


Mass: 66144.836 Da / Num. of mol.: 2
Fragment: residues 299-876 (analogous to E coli Klenow fragment)
Mutation: D598A, F710Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: polA / Plasmid: PUC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / 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

-
Non-polymers , 4 types, 801 molecules

#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-D3T / 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE


Type: DNA OH 3 prime terminus / Mass: 466.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O13P3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / 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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 50% saturated ammonium sulfate, 2.5% MPD, 100mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2MPD11
3MES11
4H2O11
5ammonium sulfate12
6ammonium sulfate12
7H2O12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.008 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 14, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 120016 / Num. obs: 120016 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rsym value: 0.111 / Χ2: 1.046 / Net I/σ(I): 14.2
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2 / Num. unique all: 11633 / Rsym value: 0.782 / Χ2: 1.025 / % possible all: 93.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LV5

1lv5


Resolution: 1.88→50 Å / Isotropic thermal model: isotropic / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 5689 4.5 %random
Rwork0.196 ---
all-120016 --
obs-113550 90.6 %-
Solvent computationBsol: 45.062 Å2
Displacement parametersBiso mean: 24.212 Å2
Baniso -1Baniso -2Baniso -3
1-0.758 Å20 Å20 Å2
2---2.216 Å20 Å2
3---1.458 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.88→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9304 810 119 794 11027
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.195
X-RAY DIFFRACTIONc_dihedral_angle_d22.15
X-RAY DIFFRACTIONc_improper_angle_d1.15
LS refinement shellResolution: 1.88→1.95 Å
RfactorNum. reflection% reflection
Rfree0.2863 510 -
Rwork0.271 --
obs-9951 80.17 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:dna-rna-multi-endo-new2.param
X-RAY DIFFRACTION4d3t.param
X-RAY DIFFRACTION5CNS_TOPPAR:sucrose.par

+
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