[English] 日本語
Yorodumi
- PDB-5a0m: THE CRYSTAL STRUCTURE OF I-SCEI IN COMPLEX WITH ITS TARGET DNA IN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5a0m
TitleTHE CRYSTAL STRUCTURE OF I-SCEI IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF MN
Components
  • (INTRON-ENCODED ENDONUCLEASE I- ...) x 2
  • 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP)-3'
  • 5'-D(*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*CP)-3'
  • 5'-D(*CP*CP*CP*TP*AP*GP*CP*GP*TP)-3'
  • 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP *AP*TP)-3'
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / GENE TARGETING / GENETICS / PROTEIN-DNA INTERACTION / HOMING ENDONUCLEASES
Function / homology
Function and homology information


Group II intron splicing / intron homing / mRNA cis splicing, via spliceosome / endonuclease activity / Hydrolases; Acting on ester bonds / mitochondrion
Similarity search - Function
LAGLIDADG DNA endonuclease family / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Intron-encoded endonuclease I-SceI
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPrieto, J. / Redondo, P. / Merino, N. / Villate, M. / Blanco, F.J. / Molina, R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Structure of the I-Scei Nuclease Complexed with its DsDNA Target and Three Catalytic Metal Ions.
Authors: Prieto, J. / Redondo, P. / Merino, N. / Villate, M. / Montoya, G. / Blanco, F.J. / Molina, R.
History
DepositionApr 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jun 29, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_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.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_asym_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INTRON-ENCODED ENDONUCLEASE I-SCEI
B: INTRON-ENCODED ENDONUCLEASE I-SCEI
C: 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP)-3'
D: 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP *AP*TP)-3'
E: 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP)-3'
H: 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP *AP*TP)-3'
I: 5'-D(*CP*CP*CP*TP*AP*GP*CP*GP*TP)-3'
J: 5'-D(*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*CP)-3'
K: 5'-D(*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*CP)-3'
L: 5'-D(*CP*CP*CP*TP*AP*GP*CP*GP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,38018
Polymers85,94010
Non-polymers4408
Water39622
1
A: INTRON-ENCODED ENDONUCLEASE I-SCEI
C: 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP)-3'
D: 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP *AP*TP)-3'
K: 5'-D(*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*CP)-3'
L: 5'-D(*CP*CP*CP*TP*AP*GP*CP*GP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2049
Polymers42,9845
Non-polymers2204
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-69.6 kcal/mol
Surface area15990 Å2
MethodPISA
2
B: INTRON-ENCODED ENDONUCLEASE I-SCEI
E: 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP)-3'
H: 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP *AP*TP)-3'
I: 5'-D(*CP*CP*CP*TP*AP*GP*CP*GP*TP)-3'
J: 5'-D(*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1769
Polymers42,9565
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-69.9 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.113, 80.565, 130.871
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
INTRON-ENCODED ENDONUCLEASE I- ... , 2 types, 2 molecules AB

#1: Protein INTRON-ENCODED ENDONUCLEASE I-SCEI / 21S RRNA INTRON MATURASE / HOMING ENDONUCLEASE OMEGA


Mass: 27717.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Gene: SCEI, OMEGA, SECY, Q0160 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): PET24D / Variant (production host): ROSETTA PLYSS
References: UniProt: P03882, Hydrolases; Acting on ester bonds
#2: Protein INTRON-ENCODED ENDONUCLEASE I-SCEI / 21S RRNA INTRON MATURASE / HOMING ENDONUCLEASE OMEGA


Mass: 27689.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Gene: SCEI, OMEGA, SECY, Q0160 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): PET24D
References: UniProt: P03882, Hydrolases; Acting on ester bonds

-
DNA chain , 4 types, 8 molecules CEDHILJK

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


Mass: 4313.831 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP *AP*TP)-3'


Mass: 4879.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#5: DNA chain 5'-D(*CP*CP*CP*TP*AP*GP*CP*GP*TP)-3'


Mass: 2691.774 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#6: DNA chain 5'-D(*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*CP)-3'


Mass: 3382.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

-
Non-polymers , 2 types, 30 molecules

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


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.11 Å3/Da / Density % sol: 48 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.89
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89 Å / Relative weight: 1
ReflectionResolution: 2.9→43.62 Å / Num. obs: 36541 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Biso Wilson estimate: 61.56 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.7 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB NETRY 2VS8

2vs8


Resolution: 2.9→42.897 Å / SU ML: 0.39 / σ(F): 0.89 / Phase error: 28.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 3649 10.19 %
Rwork0.1862 --
obs0.1926 36160 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→42.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3736 1982 8 22 5748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116046
X-RAY DIFFRACTIONf_angle_d1.2538587
X-RAY DIFFRACTIONf_dihedral_angle_d25.2522378
X-RAY DIFFRACTIONf_chiral_restr0.064940
X-RAY DIFFRACTIONf_plane_restr0.006747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.93820.4291500.33561259X-RAY DIFFRACTION100
2.9382-2.97840.37971390.32881266X-RAY DIFFRACTION100
2.9784-3.0210.35771370.29461220X-RAY DIFFRACTION100
3.021-3.06610.32861500.28241250X-RAY DIFFRACTION100
3.0661-3.11390.32341390.26231267X-RAY DIFFRACTION100
3.1139-3.1650.31381440.25481231X-RAY DIFFRACTION100
3.165-3.21950.30091380.23551283X-RAY DIFFRACTION100
3.2195-3.27810.28841370.231231X-RAY DIFFRACTION99
3.2781-3.34110.26261440.20711238X-RAY DIFFRACTION97
3.3411-3.40930.291290.20281212X-RAY DIFFRACTION98
3.4093-3.48340.28631340.19471266X-RAY DIFFRACTION99
3.4834-3.56440.26971370.20181220X-RAY DIFFRACTION100
3.5644-3.65340.24341500.19591296X-RAY DIFFRACTION100
3.6534-3.75220.2491450.19081225X-RAY DIFFRACTION100
3.7522-3.86250.28341390.19181234X-RAY DIFFRACTION100
3.8625-3.98710.26591440.18231247X-RAY DIFFRACTION100
3.9871-4.12950.26361340.18151260X-RAY DIFFRACTION100
4.1295-4.29470.21881370.15531262X-RAY DIFFRACTION100
4.2947-4.48990.23661480.1571261X-RAY DIFFRACTION100
4.4899-4.72640.21331290.15041276X-RAY DIFFRACTION100
4.7264-5.02210.21511410.16131235X-RAY DIFFRACTION100
5.0221-5.40920.23381490.15951259X-RAY DIFFRACTION100
5.4092-5.95220.18541440.151246X-RAY DIFFRACTION100
5.9522-6.81060.18771360.14871240X-RAY DIFFRACTION100
6.8106-8.56940.22831330.16421277X-RAY DIFFRACTION100
8.5694-42.90210.22431420.18741250X-RAY DIFFRACTION100

+
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