[English] 日本語
Yorodumi
- PDB-3lds: Crystal structure of RB69 gp43 with DNA and dATP opposite 8-oxoG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lds
TitleCrystal structure of RB69 gp43 with DNA and dATP opposite 8-oxoG
Components
  • DNA (5'-D(*CP*AP*(8OG)P*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
  • DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(DDG))-3')
  • DNA-directed DNA polymerase
Keywordstransferase/DNA / Protein-DNA complex / mismatch / 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 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 / : ...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 polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / 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 / Helix Hairpins / Nucleotidyltransferase; domain 5 / 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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEscherichia phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHogg, M. / Midkiff, J. / Rudnicki, J. / Reha-Krantz, L. / Doublie, S. / Wallace, S.S.
CitationJournal: Biochemistry / Year: 2010
Title: Kinetics of mismatch formation opposite lesions by the replicative DNA polymerase from bacteriophage RB69.
Authors: Hogg, M. / Rudnicki, J. / Midkiff, J. / Reha-Krantz, L. / Doublie, S. / Wallace, S.S.
History
DepositionJan 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_residues / Item: _audit_author.name
Revision 1.3Oct 13, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref / struct_ref_seq / 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 / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _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_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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
Revision 1.4Sep 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-directed DNA polymerase
P: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(DDG))-3')
T: DNA (5'-D(*CP*AP*(8OG)P*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2849
Polymers114,4353
Non-polymers8486
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-50 kcal/mol
Surface area44470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.011, 121.002, 128.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA-directed DNA polymerase / Gp43


Mass: 104613.062 Da / Num. of mol.: 1 / Mutation: D222A, D327A, L561A, I563S
Source method: isolated from a genetically manipulated source
Details: gp43 / Source: (gene. exp.) Escherichia phage RB69 (virus) / Gene: 43 / Production host: Escherichia coli (E. coli)
References: UniProt: Q38087, DNA-directed DNA polymerase, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters

-
DNA chain , 2 types, 2 molecules PT

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


Mass: 4304.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: primer
#3: DNA chain DNA (5'-D(*CP*AP*(8OG)P*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')


Mass: 5517.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: template

-
Non-polymers , 4 types, 17 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3% PEG 20000, 100mM sodium acetate, 100mM manganese acetate, 100mM Tris-HCl, 1% glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 1, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 3 Å / Num. obs: 26810

-
Processing

Software
NameVersionClassificationNB
REFMAC5.6.0041refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IG9

1ig9


Resolution: 3→29.82 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.882 / Occupancy max: 1 / Occupancy min: 0 / SU B: 42.177 / SU ML: 0.464 / Cross valid method: THROUGHOUT / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29496 1147 4.8 %RANDOM
Rwork0.24153 ---
obs0.24407 22682 91.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 94.211 Å2
Baniso -1Baniso -2Baniso -3
1--12.42 Å20 Å20 Å2
2--7.63 Å20 Å2
3---4.78 Å2
Refinement stepCycle: LAST / Resolution: 3→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7371 652 43 11 8077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0218305
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.161.91711364
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4725902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26324.16375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.828151346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3661546
X-RAY DIFFRACTIONr_chiral_restr0.0770.21172
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216123
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.030.246577
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.481 52 -
Rwork0.339 1119 -
obs--62.96 %
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)
12.48911.5283-1.055614.0824-2.86122.50230.3403-0.3204-0.14930.6398-0.5412-2.0181-0.30380.61570.20090.6637-0.123-0.30060.4140.12461.092928.4231.41-31.036
22.7265.1031-0.764110.9-3.7184.5894-0.1386-0.1337-0.4471-0.3071-0.6713-1.3432-0.01930.55930.80980.52350.0448-0.10120.24880.15010.679119.122-5.657-36.708
32.23440.1425-0.10014.2079-1.26734.28130.0151-0.2504-0.07471.0029-0.2875-0.4979-0.1609-0.02160.27240.9517-0.0244-0.37340.0650.02090.48239.033-23.687-13.8
49.41325.5744-1.63366.8816-1.15853.4007-0.79912.12290.7648-1.17320.9178-0.2104-0.375-0.3725-0.11880.8707-0.050.03890.52080.22620.19661.6290.91-56.144
55.90682.8489-0.23535.62740.33382.0013-0.80782.148-0.7913-1.52820.8513-0.33860.3493-0.3511-0.04351.1641-0.24050.11130.8359-0.24460.2112-4.91-15.506-60
62.26741.4531-0.004611.47680.28752.33-0.16970.3972-1.5344-0.499-0.0788-1.54420.86790.14220.24851.03120.15310.17010.1673-0.24831.14289.324-29.443-46.759
77.16171.3946-0.66084.40120.45054.7655-0.0452-0.5303-0.87070.32870.05120.58460.4022-0.5222-0.0060.69090.03060.05030.12650.11850.4805-22.901-21.752-28.911
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 108
2X-RAY DIFFRACTION2A340 - 382
3X-RAY DIFFRACTION3A109 - 339
4X-RAY DIFFRACTION4A383 - 468
5X-RAY DIFFRACTION5A573 - 729
6X-RAY DIFFRACTION6A469 - 572
7X-RAY DIFFRACTION7A730 - 903

+
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