[English] 日本語
Yorodumi
- PDB-5bkh: The splicing activity and an alternative domain-swapped structure... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bkh
TitleThe splicing activity and an alternative domain-swapped structure of the Pyrococcus horikoshii PolII mini-intein
ComponentsDNA polymerase II large subunit
KeywordsHYDROLASE / Intein
Function / homology
Function and homology information


exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / intein-mediated protein splicing / DNA catabolic process / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / identical protein binding
Similarity search - Function
DNA polymerase II large subunit DP2 / DNA polymerase II large subunit DP2, N-terminal / DNA polymerase II large subunit DP2 / Intein splicing domain / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. ...DNA polymerase II large subunit DP2 / DNA polymerase II large subunit DP2, N-terminal / DNA polymerase II large subunit DP2 / Intein splicing domain / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / HNH nuclease
Similarity search - Domain/homology
DNA polymerase II large subunit
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.43 Å
AuthorsLi, Z. / Li, H.
Funding support United States, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1517138 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI140726 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI141178 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA206592 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM132817 United States
CitationJournal: Sci Rep / Year: 2021
Title: An alternative domain-swapped structure of the Pyrococcus horikoshii PolII mini-intein.
Authors: Williams, J.E. / Jaramillo, M.V. / Li, Z. / Zhao, J. / Wang, C. / Li, H. / Mills, K.V.
History
DepositionMar 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase II large subunit


Theoretical massNumber of molelcules
Total (without water)21,6801
Polymers21,6801
Non-polymers00
Water43224
1
A: DNA polymerase II large subunit
x 6


Theoretical massNumber of molelcules
Total (without water)130,0786
Polymers130,0786
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area13580 Å2
ΔGint-75 kcal/mol
Surface area49080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.931, 128.931, 79.251
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-219-

HOH

-
Components

#1: Protein DNA polymerase II large subunit / / Pol II / Exodeoxyribonuclease large subunit


Mass: 21679.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: polC, PH0121 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O57861, DNA-directed DNA polymerase, exodeoxyribonuclease I
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 4.39 Å3/Da / Density % sol: 71.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris HCl, pH 8.5, with 1.8 M ammonium sulfate, 0.1 M sodium chloride, and 1% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 16787 / % possible obs: 91 % / Redundancy: 13.5 % / Biso Wilson estimate: 57.28 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.023 / Rrim(I) all: 0.077 / Χ2: 1.024 / Net I/σ(I): 8.8 / Num. measured all: 227296
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.27-2.3112.98390.6760.4350.83393.5
2.31-2.3513.58400.7370.40.84893
2.35-2.413.48400.7780.3340.8392.6
2.4-2.4513.58380.7810.3130.84693.3
2.45-2.513.58310.8690.2420.88592.70.8840.918
2.5-2.5613.68370.9010.2010.84692.60.7350.762
2.56-2.6213.58390.9070.1780.85992.60.6440.67
2.62-2.6913.68450.960.1190.89792.50.4350.451
2.69-2.7713.78160.9620.1080.88691.30.3950.41
2.77-2.8613.78380.9860.0750.928920.2740.285
2.86-2.9613.78440.9890.0641.00991.30.2340.243
2.96-3.0813.78310.990.0481.06491.20.1760.183
3.08-3.2213.78350.9950.0371.14591.10.1370.142
3.22-3.3913.88330.9970.0281.25690.60.1030.107
3.39-3.613.68410.9980.0221.271900.0810.084
3.6-3.8813.78260.9990.0181.27589.90.0670.069
3.88-4.2713.78360.9990.0171.61389.40.0640.067
4.27-4.8913.78410.9990.0141.43888.30.0520.053
4.89-6.1613.684110.0111.00187.40.040.042
6.16-5012.889610.0090.72585.10.0320.033

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
PHENIXv1.19refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.43→42.2 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2744 1366 10.01 %
Rwork0.2392 12285 -
obs0.2426 13651 90.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.77 Å2 / Biso mean: 65.2142 Å2 / Biso min: 27.66 Å2
Refinement stepCycle: final / Resolution: 2.43→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 0 24 1418
Biso mean---61.67 -
Num. residues----170
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.43-2.520.441300.39651163129388
2.52-2.620.4131370.34881235137293
2.62-2.740.31741370.29621230136792
2.74-2.880.31991350.30361221135692
2.88-3.060.34781370.31941228136591
3.06-3.30.37531370.27131242137991
3.3-3.630.32771350.26731213134890
3.63-4.150.25341370.23261231136890
4.15-5.230.19931380.16911236137489
5.23-42.20.22781430.21041286142986

+
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