[English] 日本語
Yorodumi
- PDB-5ihe: D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ihe
TitleD-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease)
ComponentsDNA polymerase II small subunit
KeywordsTRANSFERASE / DNA polymerase D-family exonuclease
Function / homology
Function and homology information


exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / DNA catabolic process / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
DNA polymerase II small subunit, archaeal / DNA polymerase delta/II small subunit family / DNA polymerase alpha/epsilon subunit B / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
ACETATE ION / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / : / DNA polymerase II small subunit
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSauguet, L. / Raia, P. / De Larue, M.
CitationJournal: Nat Commun / Year: 2016
Title: Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography.
Authors: Sauguet, L. / Raia, P. / Henneke, G. / Delarue, M.
History
DepositionFeb 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase II small subunit
B: DNA polymerase II small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,43414
Polymers107,2292
Non-polymers1,20512
Water1,18966
1
A: DNA polymerase II small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2067
Polymers53,6151
Non-polymers5926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase II small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2287
Polymers53,6151
Non-polymers6146
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.969, 91.415, 145.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase II small subunit / / Pol II


Mass: 53614.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Gene: polB, PYRAB01210, PAB2266 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V2F3, DNA-directed DNA polymerase

-
Non-polymers , 7 types, 78 molecules

#2: Chemical ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Deoxyadenosine monophosphate


Mass: 331.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O6P
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 100mM Na cacodylate pH6.7 200mM Ca Acetate 5% PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9919 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.5→48.3 Å / Num. obs: 39885 / % possible obs: 98.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 81.35 Å2 / Rsym value: 0.061 / Net I/σ(I): 6.9
Reflection shellResolution: 2.5→2.64 Å / Rsym value: 0.825

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→47.42 Å / Cor.coef. Fo:Fc: 0.9477 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.396 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.38 / SU Rfree Blow DPI: 0.233 / SU Rfree Cruickshank DPI: 0.239
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 1998 5.01 %RANDOM
Rwork0.1974 ---
obs0.1988 39885 98.92 %-
Displacement parametersBiso mean: 86.01 Å2
Baniso -1Baniso -2Baniso -3
1--5.6418 Å20 Å20 Å2
2---5.1597 Å20 Å2
3---10.8014 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7050 0 63 66 7179
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087283HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.089902HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2487SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes177HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1056HARMONIC5
X-RAY DIFFRACTIONt_it7283HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion17.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion924SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8075SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2398 129 4.4 %
Rwork0.2395 2804 -
all0.2395 2933 -
obs--99.53 %
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)
10.76530.34660.68311.9724-0.77452.9238-0.30230.2307-0.0158-0.24130.16530.09-0.1780.06670.1371-0.1640.06090.03260.00540.0162-0.294667.72872.51646.3622
22.4121-0.23650.58811.95550.46732.3288-0.092-0.1492-0.4123-0.0978-0.0713-0.26070.19030.1480.1633-0.23130.06480.0894-0.22490.0847-0.112943.856943.06174.5925
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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