[English] 日本語
Yorodumi
- PDB-4e2u: Crystal Structures of RadAmin intein from Pyrococcus horikoshii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e2u
TitleCrystal Structures of RadAmin intein from Pyrococcus horikoshii
ComponentsPho radA intein
KeywordsUNKNOWN FUNCTION / HINT-fold
Function / homology
Function and homology information


DNA recombinase assembly / mitotic recombination / DNA strand invasion / intein-mediated protein splicing / DNA strand exchange activity / ATP-dependent DNA damage sensor activity / single-stranded DNA binding / double-stranded DNA binding / damaged DNA binding / ATP binding
Similarity search - Function
Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / DNA recombination/repair protein RadA / Intein splicing domain / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region ...Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / DNA recombination/repair protein RadA / Intein splicing domain / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / 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 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.582 Å
AuthorsOeemig, J.S. / Zhou, D. / Kajander, T. / Wlodawer, A. / Iwai, H.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: NMR and Crystal Structures of the Pyrococcus horikoshii RadA Intein Guide a Strategy for Engineering a Highly Efficient and Promiscuous Intein.
Authors: Oeemig, J.S. / Zhou, D. / Kajander, T. / Wlodawer, A. / Iwai, H.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pho radA intein


Theoretical massNumber of molelcules
Total (without water)19,1331
Polymers19,1331
Non-polymers00
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.930, 63.649, 66.552
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Pho radA intein / DNA repair and recombination protein radA


Mass: 19132.527 Da / Num. of mol.: 1 / Mutation: S150Q, G151H, K152M, C153A, K283N, T325A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: radA, PH0263 / Plasmid: pCARSF15 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: O58001
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 1.6 M tri-sodium citrate, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 13, 2011
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.58→46 Å / Num. all: 28054 / Num. obs: 27745 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Rmerge(I) obs: 0.086
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.454 / % possible all: 89.6

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E2T

4e2t


Resolution: 1.582→38.364 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 17.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 887 3.2 %RANDOM
Rwork0.1674 ---
obs0.1683 27680 99.28 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.078 Å2 / ksol: 0.401 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9708 Å2-0 Å20 Å2
2---6.0283 Å2-0 Å2
3---3.0574 Å2
Refinement stepCycle: LAST / Resolution: 1.582→38.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 0 251 1602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111401
X-RAY DIFFRACTIONf_angle_d1.3991908
X-RAY DIFFRACTIONf_dihedral_angle_d12.185515
X-RAY DIFFRACTIONf_chiral_restr0.1211
X-RAY DIFFRACTIONf_plane_restr0.008246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5821-1.68130.28241470.23254239X-RAY DIFFRACTION96
1.6813-1.81110.20721400.18224435X-RAY DIFFRACTION100
1.8111-1.99330.18641510.14974439X-RAY DIFFRACTION100
1.9933-2.28180.17131450.15154464X-RAY DIFFRACTION100
2.2818-2.87470.19451420.16724531X-RAY DIFFRACTION100
2.8747-46.01810.19221620.16684685X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 3.1164 Å / Origin y: 9.2798 Å / Origin z: 6.8406 Å
111213212223313233
T0.0644 Å2-0.0019 Å20.0098 Å2-0.0861 Å2-0.0015 Å2--0.085 Å2
L0.357 °2-0.0959 °2-0.0256 °2-0.9417 °20.063 °2--0.7385 °2
S0.0086 Å °-0.0006 Å °-0.0019 Å °-0.0335 Å °0.0194 Å °0.0475 Å °-0.005 Å °0.0089 Å °0 Å °
Refinement TLS groupSelection details: (chain A and resid -3:174)

+
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